Estimation of the Quality of Refined Protein Crystal Structures
Jimin Wang
Supplementary text (1 paragraph, 7 tables, and 16 references)
All analysis was carried out using the data retrieved in April, 2014. References for entries
enlisted in Table 4 with very high <I/I> values in the highest resolution shells are as
follows: 2IQ0,1 3VI1,2 1A7E,3 1A7D,3 1COB,4 1RTA,5 1LNZ,6 1DTM,7 2ZRS,8 2F3G,9
1DUO,7 1DUK,7 2ABH,10 2ISF,1 2ZRT,8 1GQ3,11 1CRB,12 and 3W55.13 It is almost
certain that not all these entries resulted from clerical errors. Even so, it is not excusable,
especially for making multiple clerical errors from the same laboratory. For example,
Rwork was reported to be 0.05 for 2IUJ at a resolution of 2.4 Å and Rwork was 0.055 for
2J3J at a resolution of 2.8 Å, both of which are statistically impossible without some kind
of statistical gaming.14,15 Other such entries include 1XZD with Rwork of 0.099 at a
resolution of 2.70 Å.16
Supplemental Tables
Table SI. Solvent Contents for Macromolecular Crystalsa
Space group
Percentage(%) Solvent Content(%)
All
100.0
50.28.6
P212121
23.0
48.28.5
P21
15.4
47.18.0
C2
9.6
50.79.0
P21212
5.7
49.58.0
C2221
4.9
52.89.2
P1
4.6
47.88.1
P43212
3.7
51.710.4
P3221
3.3
56.09.3
P41212
3.2
55.110.4
P3121
3.2
56.610.8
I222
2.1
54.49.8
P6122
1.7
56.69.4
H32
1.5
H3
1.5
P6522
1.3
57.49.7
P61
1.1
P65
1.0
5-Å resolution or lower
0.18
70.29.9
4-Å resolution or lower
0.57
67.610.3
3.5-Å resolution or lower 1.81
65.210.1
3.2-Å resolution or lower 4.08
62.810.2
3-Å resolution or lower
7.54
60.89.9
1-Å resolution or higher 0.65
39.09.2
Footnotes:
a
No attempt was made to correct assignment errors of space groups.
2
Table SII. Lattice system distribution
Lattice systems
Percentage (%)
Triclinic
4.6
Monoclinic
25.3
Orthorhombic
36.4
Tetragonal
12.4
Rhombohedral
3.0
Hexagonal/Trigonal 16.5
Cubic
2.0
Primitive
76.4
C-centered
14.7
I-centered
5.42
F-centered
0.50
Table SIII. Solvent Contents for Macromolecular Crystals in Point-Symmetry Groups
Space group Percentage(%) Solvent Content(%)
P1
76.4
47.88.1
P2
3.17
49.97.4
P3
3.19
52.49.1
P4
1.76
53.68.4
P6
4.58
57.87.5
P222
0.22
56.09.2
P312
0.28
56.09.6
P321
6.46
58.09.7
P422
0.83
57.47.7
P622
1.41
59.99.3
P23
0.98
60.69.3
P432
0.73
60.28.3
Subtotal
5,326 entries
I222
73.1
54.59.8
I422
22.8
57.39.3
I432
4.07
60.77.3
Subtotal
2,570 entries
F222
39.2
54.910.0
F432
60.8
61.17.1
Subtotal
297 entries
3
Table SIV. Selected P212121 entries with very large <I/I> values at their highest
resolution shells.
Accession
2IQ0
3VI1
1A7E
1A7D
1COB
1RTA
1LNZ
1DTM
2ZRS
2F3G
1DUO
1DUK
2ABH
2ISF
2ZRT
1GQ3
1CRB
3W55
2NYX
2VRC
1LTS
3JYY
4ITD
2VVK
1Y97
2E5V
2ZC0
2LZH
3BDB
3CZC
2W3D
1XNI
Resolution (Å)
1.95
2.00
1.74
1.74
2.03
2.50
2.60
2.13
3.10
2.13
1.96
2.13
1.67
2.00
3.30
2.01
2.15
3.00
2.30
2.50
1.94
1.90
1.94
1.60
2.50
2.09
2.30
5.91
2.81
2.02
2.00
2.80
<I/I>
810.147
790.842
641.941
610.056
577.711
364.000
322.826
283.104
278.470
245.330
171.612
160.688
140.621
100.740
99.500
98.082
91.888
91.719
91.355
85.871
81.188
79.993
76.308
74.406
72.981
66.044
63.687
61.454
61.400
53.000
52.561
51.705
4
Table SV. Original structure factors for the selected P212121 entries with very large <I/I> values at their highest resolution shells
(continuous double columns for the entire table)a.
__________________________________________________________________________________________________________
2IQ0:
loop_
_refln.crystal_id
_refln.wavelength_id
_refln.scale_group_code
_refln.index_h
_refln.index_k
_refln.index_l
_refln.status
_refln.F_meas_au
_refln.F_meas_sigma_au
1 1 1
22
0
0 o
387.73
1 1 1
24
0
0 o
276.25
1 1 1
19
1
0 o
452.95
1 1 1
20
1
0 o
65.83
1 1 1
21
1
0 o
326.88
1 1 1
22
1
0 o
231.71
1 1 1
23
1
0 o
341.97
1 1 1
3
2
0 f
260.88
1 1 1
4
2
0 o
108.40
1 1 1
5
2
0 o 1030.64
3VI1:
loop_
_refln.crystal_id
_refln.wavelength_id
_refln.scale_group_code
_refln.index_h
_refln.index_k
_refln.index_l
_refln.status
_refln.F_meas_au
_refln.F_meas_sigma_au
_refln.F_calc
_refln.phase_calc
_refln.fom
1 1 1
4
0
0 x
1 1 1
6
0
0 x
1 1 1
8
0
0 o
1 1 1
10
0
0 o
1 1 1
12
0
0 x
?
?
318.4
161.9
?
0.05
0.07
0.05
0.40
0.07
0.05
0.04
0.05
0.07
0.07
2F3G:
loop_
_refln.crystal_id
_refln.wavelength_id
_refln.scale_group_code
_refln.index_h
_refln.index_k
_refln.index_l
_refln.status
_refln.F_meas_au
_refln.F_meas_sigma_au
1 1 1
0
0
2 o
1 1 1
0
0
3 o
1 1 1
0
0
4 o
1 1 1
0
0
5 o
1 1 1
0
0
6 o
1 1 1
0
0
7 o
1 1 1
0
0
8 o
1 1 1
0
0
9 o
1 1 1
0
0
12 o
1 1 1
0
0
13 o
0.0
128.0
404.0
88.0
981.0
176.0
1513.0
88.0
692.0
172.0
1.0
0.6
0.3
2.2
0.3
1.5
0.3
3.9
0.6
3.0
?
?
1.2
4.4
?
1DUO:
loop_
_refln.crystal_id
_refln.wavelength_id
_refln.scale_group_code
_refln.index_h
_refln.index_k
_refln.index_l
_refln.status
_refln.F_meas_au
_refln.F_meas_sigma_au
1 1 1
0
0
4 o
1 1 1
0
0
6 o
1 1 1
0
0
8 o
1 1 1
0
0
10 o
1 1 1
0
0
12 o
1 1 1
0
0
14 o
1 1 1
0
0
16 o
1 1 1
0
0
18 o
4910.000
6057.000
1618.000
1864.000
3068.000
3064.000
1944.000
8342.000
0.700
0.800
0.500
0.600
0.600
0.700
0.800
0.700
5377.7
6122.5
1797.9
612.3
328.3
180.0
360.0
180.0
0.0
180.0
0.00
0.00
0.99
0.66
0.00
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
14
16
18
20
22
0
0
0
0
0
0
0
0
0
0
o
x
x
x
o
0.1
?
?
?
2205.7
1A7E:
loop_
_refln.crystal_id
_refln.wavelength_id
_refln.scale_group_code
_refln.index_h
_refln.index_k
_refln.index_l
_refln.status
_refln.F_meas_au
_refln.F_meas_sigma_au
_refln.phase_meas
_refln.weight
1 1 1
6
0
0 o 9889.628
1 1 1
8
0
0 o 1508.128
1 1 1
10
0
0 o 690.503
1 1 1
12
0
0 f 4271.080
1 1 1
14
0
0 f 1831.316
1 1 1
16
0
0 o 1754.869
1 1 1
18
0
0 o 5400.063
1 1 1
22
0
0 o 855.831
1 1 1
5
1
0 o 1571.423
1 1 1
6
1
0 o 4063.078
1A7D:
loop_
_refln.crystal_id
_refln.wavelength_id
_refln.scale_group_code
_refln.index_h
_refln.index_k
_refln.index_l
_refln.status
_refln.F_meas_au
_refln.F_meas_sigma_au
_refln.phase_meas
_refln.weight
1 1 1
6
0
0 o 8614.116
1 1 1
8
0
0 o 1344.299
1 1 1
10
0
0 o 446.748
1 1 1
12
0
0 f 4507.882
199.3
?
?
?
1.1
1.000
1.000
1.000
1.000
1.000
1.000
1.000
1.000
1.000
1.000
1.000
1.000
1.000
1.000
379.6
168.1
343.9
424.1
1786.4
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
360.0
180.0
180.0
0.0
180.0
1.000
1.000
1.000
1.000
1.000
1.000
1.000
1.000
1.000
1.000
1.000
1.000
1.000
1.000
0.00
0.00
0.00
0.00
1.00
1 1 1
1 1 1
0
0
0
0
20
22
o 1811.000
o 1258.000
0.700
1.500
1DUK:
loop_
_refln.crystal_id
_refln.wavelength_id
_refln.scale_group_code
_refln.index_h
_refln.index_k
_refln.index_l
_refln.status
_refln.F_meas_au
_refln.F_meas_sigma_au
1 1 1
0
0
4 o
1 1 1
0
0
6 o
1 1 1
0
0
8 o
1 1 1
0
0
10 o
1 1 1
0
0
12 o
1 1 1
0
0
14 o
1 1 1
0
0
16 o
1 1 1
0
0
18 o
1 1 1
0
0
20 o
1 1 1
0
0
22 o
3972.000
4557.000
1522.000
1784.000
2352.000
2722.000
1959.000
6555.000
1263.000
411.000
2ABH:
loop_
_refln.crystal_id
_refln.wavelength_id
_refln.scale_group_code
_refln.index_h
_refln.index_k
_refln.index_l
_refln.status
_refln.F_meas_au
_refln.F_meas_sigma_au
1 1 1
4
0
0 o
1 1 1
6
0
0 o
1 1 1
8
0
0 o
1 1 1
10
0
0 o
1 1 1
12
0
0 o
1 1 1
14
0
0 o
1 1 1
16
0
0 o
1 1 1
18
0
0 o
1 1 1
20
0
0 o
1 1 1
3
1
0 o
377.50311 0.04765
250.38260 0.07148
88.39870 0.09531
622.85602 0.11913
239.77199 0.14296
177.62421 0.16679
54.49990 0.19061
142.55411 0.21444
84.74700 0.23827
187.75250 0.03658
6
0.500
0.700
0.700
0.800
0.800
0.800
1.200
1.000
2.600
7.200
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
14
16
18
20
22
0
0
0
0
0
0
0
0
0
0
o
f
o
o
o
1350.233
2239.096
6531.295
519.671
1707.239
1COB:
loop_
_refln.crystal_id
_refln.wavelength_id
_refln.scale_group_code
_refln.index_h
_refln.index_k
_refln.index_l
_refln.status
_refln.F_meas_au
_refln.F_meas_sigma_au
1 1 1
0
0
4 o
1 1 1
0
0
8 o
1 1 1
0
0
12 o
1 1 1
0
1
5 o
1 1 1
0
1
6 o
1 1 1
0
1
7 o
1 1 1
0
1
8 o
1 1 1
0
1
10 o
1 1 1
0
1
11 o
1 1 1
0
1
12 o
1 1 1
0
1
13 o
1 1 1
0
1
14 o
1 1 1
0
1
15 o
1RTA:
loop_
_refln.crystal_id
_refln.wavelength_id
_refln.scale_group_code
_refln.index_h
_refln.index_k
_refln.index_l
_refln.status
_refln.F_meas_au
_refln.F_meas_sigma_au
1 1 1
0
0
2 o
1 1 1
0
0
4 o
1 1 1
0
0
6 o
1 1 1
0
0
8 o
1 1 1
0
0
10 o
274.200
34.300
426.700
548.300
860.800
398.500
799.100
434.200
451.600
816.100
271.200
692.100
779.400
1.000
1.000
1.000
1.000
1.000
0.000
0.100
0.100
0.100
0.100
0.100
0.100
0.100
0.100
0.100
0.100
0.100
0.200
2.381 -0.009
2.361 -0.009
10.731 0.029
5.067 0.003
3.428 -0.004
0.000
0.000
0.000
0.000
0.000
1.000
1.000
1.000
1.000
1.000
2ISF:
loop_
_refln.crystal_id
_refln.wavelength_id
_refln.scale_group_code
_refln.index_h
_refln.index_k
_refln.index_l
_refln.status
_refln.F_meas_au
_refln.F_meas_sigma_au
1 1 1
2
0
0 o
1 1 1
6
0
0 o
1 1 1
8
0
0 o
1 1 1
10
0
0 o
1 1 1
12
0
0 o
1 1 1
14
0
0 o
1 1 1
18
0
0 o
1 1 1
20
0
0 o
1 1 1
2
1
0 o
1 1 1
3
1
0 o
112.10
71.11
53.82
55.79
29.39
24.82
66.61
46.52
5.01
138.28
0.03
0.02
0.02
0.02
0.06
0.09
0.03
0.05
0.28
0.01
2ZRT:
loop_
_refln.crystal_id
_refln.wavelength_id
_refln.scale_group_code
_refln.index_h
_refln.index_k
_refln.index_l
_refln.status
_refln.F_meas_au
_refln.F_meas_sigma_au
_refln.F_calc
_refln.phase_calc
_refln.fom
1 1 1
0
0
2 o
1 1 1
0
0
4 o
1 1 1
0
0
6 o
1 1 1
0
0
8 o
1 1 1
0
0
10 o
1 1 1
0
0
12 o
1 1 1
0
0
14 o
1 1 1
0
0
16 o
1 1 1
0
0
18 o
1 1 1
0
0
20 o
2452.4
2483.8
350.0
304.4
1709.5
1247.7
139.2
1195.4
822.9
130.0
1.1
1.1
0.9
1.1
1.1
0.6
0.0
1.1
1.0
0.8
7
4019.9
41350.7
2224.7
2171.3
2960.2
4164.0
988.6
2183.5
3014.1
103.7
180.0
0.0
180.0
0.0
0.0
0.0
180.0
0.0
180.0
0.0
1.00
1.00
0.08
0.33
1.00
0.99
0.06
0.99
0.91
0.08
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
0
0
0
0
0
0
1
1
1
1
16
2
3
4
5
o
o
o
o
o
1LNZ:
loop_
_refln.crystal_id
_refln.wavelength_id
_refln.scale_group_code
_refln.index_h
_refln.index_k
_refln.index_l
_refln.status
_refln.F_meas_au
_refln.F_meas_sigma_au
1 1 1
0
0
8 o
1 1 1
0
0
10 o
1 1 1
0
0
12 o
1 1 1
0
0
14 o
1 1 1
0
0
16 o
1 1 1
0
0
18 o
1 1 1
0
0
20 o
1 1 1
0
0
22 o
1 1 1
0
0
24 o
1 1 1
0
0
26 o
1DTM:
loop_
_refln.crystal_id
_refln.wavelength_id
_refln.scale_group_code
_refln.index_h
_refln.index_k
_refln.index_l
_refln.status
_refln.F_meas_au
_refln.F_meas_sigma_au
1 1 1
0
0
6 o
1 1 1
0
0
8 o
1 1 1
0
0
10 o
1 1 1
0
0
12 o
1 1 1
0
0
14 o
1 1 1
0
0
16 o
1 1 1
0
0
18 o
1 1 1
0
0
20 o
3.503 -0.004
6.136 0.008
5.138 0.004
5.406 0.005
5.951 0.007
144.1
1192.9
432.1
1016.0
530.4
695.6
849.9
258.3
167.4
733.1
7356.000
1583.000
2631.000
3084.000
3524.000
1333.000
9862.000
2435.000
0.51
1.00
1.00
1.00
1.00
1.00
1.00
0.80
0.41
0.02
1.000
0.300
0.400
0.500
0.600
0.500
0.900
0.400
1GQ3:
loop_
_refln.crystal_id
_refln.wavelength_id
_refln.scale_group_code
_refln.index_h
_refln.index_k
_refln.index_l
_refln.status
_refln.F_meas_au
_refln.F_meas_sigma_au
1 1 1
0
0
46 o
35.86
1 1 1
0
0
48 o
484.75
1 1 1
0
0
50 o
783.85
1 1 1
0
0
54 o
665.94
1 1 1
0
0
56 o
967.96
1 1 1
0
0
58 o
425.74
1 1 1
0
0
60 o
420.77
1 1 1
0
0
62 o 1304.05
1 1 1
0
0
64 o
366.54
1 1 1
0
0
66 o
325.61
0.03
0.79
0.84
0.85
0.90
0.82
0.86
0.90
0.90
0.78
1CRB:
loop_
_refln.crystal_id
_refln.wavelength_id
_refln.scale_group_code
_refln.index_h
_refln.index_k
_refln.index_l
_refln.status
_refln.F_meas_au
_refln.F_meas_sigma_au
1 1 1
12
0
0 o
1 1 1
14
0
0 o
1 1 1
16
0
0 o
1 1 1
18
0
0 o
1 1 1
4
1
0 o
1 1 1
5
1
0 o
1 1 1
6
1
0 o
1 1 1
7
1
0 o
1 1 1
8
1
0 o
1 1 1
9
1
0 o
1.000
1.000
1.000
1.000
1.000
1.000
1.000
1.000
1.000
1.000
3W55:
loop_
_refln.crystal_id
8
467.070
170.320
112.850
417.240
458.590
146.750
91.450
414.920
198.170
643.660
1 1 1
1 1 1
0
0
0
0
22
24
o 2306.000
o 970.000
0.400
1.100
_refln.wavelength_id
_refln.scale_group_code
_refln.index_h
_refln.index_k
_refln.index_l
_refln.status
_refln.F_meas_au
_refln.F_meas_sigma_au
1 1 1
0
0
6 o
353.00
1 1 1
0
0
8 o
304.00
1 1 1
0
0
10 o
639.00
1 1 1
0
0
12 f
41.00
1 1 1
0
0
14 o 1017.00
1 1 1
0
0
16 o
736.00
1 1 1
0
0
18 f
162.00
1 1 1
0
0
20 o
171.00
1 1 1
0
0
22 f
254.00
1 1 1
0
0
24 o
193.00
2ZRS:
loop_
_refln.crystal_id
_refln.wavelength_id
_refln.scale_group_code
_refln.index_h
0.80
_refln.index_k
0.60
_refln.index_l
0.20
_refln.status
0.50
_refln.F_meas_au
0.00
_refln.F_meas_sigma_au
0.70
_refln.F_calc
0.30
_refln.phase_calc
0.20
_refln.fom
0.50
1 1 1
0
0
4 o
5453.9
0.9
46470.0
0.0 1.00
0.10
1 1 1
0
0
6 o
2811.9
0.9
12329.6
0.0 1.00
1 1 1
0
0
8 o
3653.5
0.9
11131.2
180.0 1.00
1 1 1
0
0
10 o
4019.0
0.9
10444.8
0.0 1.00
1 1 1
0
0
12 o
2430.7
0.9
6996.3
0.0 1.00
1 1 1
0
0
14 o
379.2
0.5
1306.2
180.0 0.13
1 1 1
0
0
16 o
2657.4
0.9
7085.0
180.0 1.00
1 1 1
0
0
18 o
622.5
0.9
1550.2
180.0 0.06
1 1 1
0
0
20 o
1307.1
0.9
2558.0
180.0 1.00
1 1 1
0
0
22 o
531.1
0.8
339.4
180.0 0.02
____________________________________________________________________________________________________________________________________
Footnotes:
a
In these selected entries, each file includes about the first 10 to 12 reflections to demonstrate some unusual features in the
standard deviations of measured amplitudes: (i) a single uniformed number, (ii) two, three or a few variations only, (iii) different
significant decimals from amplitudes, and; (iv) negative numbers.. Entries without observed deviations cannot be analyzed and are
thus rejected.
9
Table SVI. The low-resolution cut-off among all P212121 entries analyzed in the PDB.
Low resolution cut-off
8.0 Å
7.0 Å
6.0 Å
5.0 Å
Number (percentage)
777 (5.1%)
286 (1.8%)
189 (1.2%)
32 (0.2%)
10
Table SVII. Selected P212121 entries with very small free and working R-factor
differences
Accession
1CXE
1D8F
1D7X
4A9V
1SRP
2B12
297D
2W6E
3UYN
1U93
4AR2
2W6F
1CVY
1FVT
1PIO
1SQT
1US8
1XB4
1ZCD
2QPY
2YWW
3IDJ
3NTT
3TMT
1KAQ
1N8E
1ZS8
2ATO
2OF2
2W6I
4BFH
1P5W
1X36
1XPB
3G2A
1E7O
1HAZ
1L8V
1UCD
1XOW
1XXI
1Y2F
2OXS
2RI7
2ZZQ
3IDG
3UI4
1E6G
1GCI
1U8O
2VPW
2VPZ
2ZTN
3AKQ
3E21
3K59
3UT8
Resolution (Å)
2.10
2.40
2.00
1.10
2.00
3.02
2.50
6.50
2.60
2.37
3.80
6.00
2.15
2.20
2.80
1.90
2.10
3.10
3.45
2.50
2.00
2.24
3.45
2.00
3.20
4.50
3.00
2.00
2.00
4.00
1.25
3.30
2.70
1.90
2.00
3.20
1.40
2.80
1.30
1.80
4.10
2.00
1.32
1.45
3.81
1.86
0.80
2.30
0.78
3.02
3.10
2.40
3.56
0.97
1.73
1.92
2.17
Rworking
0.153
0.294
0.262
0.137
0.193
0.277
0.221
0.290
0.206
0.238
0.280
0.345
0.229
0.232
0.189
0.236
0.219
0.327
0.316
0.269
0.226
0.229
0.252
0.295
0.279
0.415
0.307
0.197
0.260
0.299
0.158
0.200
0.245
0.156
0.239
0.234
0.199
0.290
0.200
0.210
0.366
0.225
0.155
0.189
0.242
0.224
0.095
0.267
0.099
0.211
0.271
0.249
0.305
0.200
0.218
0.198
0.223


-0.042
-0.035
-0.019
-0.009
-0.009
-0.005
-0.005
-0.005
-0.003
-0.002
-0.002
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.001
0.001
0.001
0.001
0.001
0.001
0.001
0.002
0.002
0.002
0.002
0.003
0.003
0.003
0.003
0.003
0.003
0.003
0.003
0.003
0.003
0.003
0.003
0.004
0.004
0.004
0.004
0.004
0.004
0.004
0.004
0.004
0.004
Rfree
0.100
0.252
0.227
0.117
0.184
0.268
0.216
0.285
0.201
0.235
0.278
0.343
0.229
0.232
0.189
0.236
0.219
0.327
0.316
0.269
0.226
0.229
0.252
0.295
0.280
0.416
0.308
0.198
0.261
0.300
0.159
0.202
0.247
0.158
0.241
0.237
0.202
0.293
0.203
0.213
0.369
0.228
0.158
0.192
0.245
0.227
0.098
0.271
0.103
0.215
0.275
0.253
0.309
0.204
0.222
0.202
0.227
11

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13