- PDB-4ql5: Crystal structure of translation initiation factor IF-1 from Stre... -
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ID or keywords:
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Basic information
Entry
Database: PDB / ID: 4ql5
Title
Crystal structure of translation initiation factor IF-1 from Streptococcus pneumoniae TIGR4
Components
Translation initiation factor IF-1
Keywords
TRANSLATION / translation initiation factor / PROTEIN BIOSYNTHESIS / NIAID / NATIONAL INSTITUTE OF ALLERGY AND INFECTIOUS DISEASES / CSGID / CENTER FOR STRUCTURAL GENOMICS OF INFECTIOUS DISEASES / STRUCTURAL GENOMICS / BETA BARREL / OB FOLD
Resolution: 2.02→2.22 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.478 / Mean I/σ(I) obs: 3.4 / Num. unique all: 2827 / % possible all: 99.6
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Processing
Software
Name
Version
Classification
HKL-3000
datacollection
PHENIX
(phenix.autsol)
modelbuilding
PHENIX
(phenix.refine: 1.9_1692)
refinement
XDS
datareduction
Aimless
datascaling
PHENIX
phasing
Refinement
Method to determine structure: SAD / Resolution: 2.025→19.323 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.39 / Stereochemistry target values: ML
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.2091
1071
4.81 %
random
Rwork
0.1885
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-
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obs
0.1895
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99.84 %
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Solvent computation
Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement step
Cycle: LAST / Resolution: 2.025→19.323 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
1071
0
12
97
1180
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
X-RAY DIFFRACTION
f_bond_d
0.007
1120
X-RAY DIFFRACTION
f_angle_d
1.11
1508
X-RAY DIFFRACTION
f_dihedral_angle_d
14.128
440
X-RAY DIFFRACTION
f_chiral_restr
0.032
174
X-RAY DIFFRACTION
f_plane_restr
0.005
192
LS refinement shell
Resolution (Å)
Rfactor Rfree
Num. reflection Rfree
Rfactor Rwork
Num. reflection Rwork
Refine-ID
% reflection obs (%)
2.0247-2.1167
0.2956
149
0.284
2609
X-RAY DIFFRACTION
99
2.1167-2.2282
0.2558
124
0.2574
2665
X-RAY DIFFRACTION
100
2.2282-2.3676
0.2842
139
0.2346
2643
X-RAY DIFFRACTION
100
2.3676-2.55
0.2836
129
0.245
2656
X-RAY DIFFRACTION
100
2.55-2.8059
0.2774
127
0.2427
2666
X-RAY DIFFRACTION
100
2.8059-3.2103
0.1962
143
0.2044
2649
X-RAY DIFFRACTION
100
3.2103-4.0386
0.2157
121
0.1764
2656
X-RAY DIFFRACTION
100
4.0386-19.3236
0.1578
139
0.1411
2652
X-RAY DIFFRACTION
100
Refinement TLS params.
Method: refined / Refine-ID: X-RAY DIFFRACTION
ID
L11 (°2)
L12 (°2)
L13 (°2)
L22 (°2)
L23 (°2)
L33 (°2)
S11 (Å °)
S12 (Å °)
S13 (Å °)
S21 (Å °)
S22 (Å °)
S23 (Å °)
S31 (Å °)
S32 (Å °)
S33 (Å °)
T11 (Å2)
T12 (Å2)
T13 (Å2)
T22 (Å2)
T23 (Å2)
T33 (Å2)
Origin x (Å)
Origin y (Å)
Origin z (Å)
1
6.8632
-5.8577
-0.5067
5.4503
-0.6484
2.6391
-0.264
0.3912
1.8898
1.7758
0.0677
-1.2845
-1.2437
-0.7733
0.132
0.7221
0.0336
-0.0063
0.4408
0.0555
0.5385
48.5328
37.2833
32.5459
2
0.5063
-0.7752
0.8693
1.431
-0.3107
5.5056
0.2809
-0.0449
-0.1144
-0.4357
0.3199
0.3983
0.49
-0.8653
-0.6236
0.5556
-0.1381
-0.0476
0.498
0.0997
0.3958
43.7592
26.7815
27.0601
3
4.055
-0.5816
-0.4735
8.8664
1.5393
5.9936
-0.3959
-0.7181
0.5739
-0.2093
0.6461
0.5188
-0.0107
-0.5574
-0.2161
0.4606
0.0251
-0.0924
0.615
0.0337
0.3669
44.702
31.9941
28.7475
4
3.0509
1.4262
3.1908
2.8808
-0.6586
8.1775
0.5134
0.0301
0.5207
-0.0999
-0.6268
0.2746
-0.1888
-0.1168
0.0769
0.3804
0.0127
0.0556
0.2811
0.0307
0.3716
61.3376
42.4841
22.5075
5
9.0086
2.2237
-2.2417
6.9365
-1.1484
4.9064
0.2449
-0.0059
0.4885
-0.1593
-0.1198
-0.3092
-0.2507
0.3297
-0.0925
0.3022
-0.0199
-0.0338
0.2366
0.0254
0.2879
66.1738
43.7227
21.0946
6
4.2835
-2.4628
-0.4246
9.4096
-0.9765
3.1377
-0.3402
-0.1404
0.1001
0.2767
-0.0834
-0.3652
-0.0789
0.8449
0.479
0.2655
-0.0023
0.0008
0.4332
0.0834
0.3306
67.7389
37.4649
22.3665
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Selection details
1
X-RAY DIFFRACTION
1
(chainAandresid5:10)
2
X-RAY DIFFRACTION
2
(chainAandresid11:59)
3
X-RAY DIFFRACTION
3
(chainAandresid60:72)
4
X-RAY DIFFRACTION
4
(chainBandresid8:17)
5
X-RAY DIFFRACTION
5
(chainBandresid18:55)
6
X-RAY DIFFRACTION
6
(chainBandresid56:72)
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