- PDB-3b7h: Crystal structure of the prophage Lp1 protein 11 -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 3b7h
Title
Crystal structure of the prophage Lp1 protein 11
Components
Prophage Lp1 protein 11
Keywords
STRUCTURAL PROTEIN / prophage Lp1 protein 11 / structural genomics / PSI2 / MCSG / Protein Structure Initiative / Midwest Center for Structural Genomics
Monochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.9794 Å / Relative weight: 1
Reflection
Resolution: 2→36.51 Å / Num. all: 5420 / Num. obs: 5218 / % possible obs: 96.27 % / Observed criterion σ(I): 2 / Redundancy: 8 % / Biso Wilson estimate: 24.5 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 32.74
Reflection shell
Resolution: 2→2.053 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.282 / Mean I/σ(I) obs: 4.85 / Num. unique all: 405 / % possible all: 79.75
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Processing
Software
Name
Version
Classification
REFMAC
5.2.0019
refinement
SBC-Collect
datacollection
HKL-3000
datareduction
HKL-3000
datascaling
MLPHARE
phasing
Refinement
Method to determine structure: SAD / Resolution: 2→36.51 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.919 / SU B: 11.555 / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.182 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.24945
251
4.6 %
RANDOM
Rwork
0.1956
-
-
-
all
0.19816
5218
-
-
obs
0.19816
5218
96.27 %
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Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parameters
Biso mean: 24.522 Å2
Baniso -1
Baniso -2
Baniso -3
1-
1.66 Å2
0 Å2
0 Å2
2-
-
-1.59 Å2
0 Å2
3-
-
-
-0.07 Å2
Refinement step
Cycle: LAST / Resolution: 2→36.51 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
597
0
0
60
657
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.015
0.022
607
X-RAY DIFFRACTION
r_bond_other_d
0.001
0.02
406
X-RAY DIFFRACTION
r_angle_refined_deg
1.497
1.95
821
X-RAY DIFFRACTION
r_angle_other_deg
0.99
3
993
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
5.228
5
75
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
32.567
24.286
28
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
14.472
15
107
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
11.287
15
4
X-RAY DIFFRACTION
r_chiral_restr
0.077
0.2
97
X-RAY DIFFRACTION
r_gen_planes_refined
0.005
0.02
667
X-RAY DIFFRACTION
r_gen_planes_other
0.001
0.02
121
X-RAY DIFFRACTION
r_nbd_refined
0.221
0.2
151
X-RAY DIFFRACTION
r_nbd_other
0.185
0.2
407
X-RAY DIFFRACTION
r_nbtor_refined
0.186
0.2
308
X-RAY DIFFRACTION
r_nbtor_other
0.089
0.2
287
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.221
0.2
46
X-RAY DIFFRACTION
r_symmetry_vdw_refined
0.243
0.2
11
X-RAY DIFFRACTION
r_symmetry_vdw_other
0.284
0.2
45
X-RAY DIFFRACTION
r_symmetry_hbond_refined
0.092
0.2
10
X-RAY DIFFRACTION
r_mcbond_it
1.397
1.5
486
X-RAY DIFFRACTION
r_mcbond_other
0.474
1.5
153
X-RAY DIFFRACTION
r_mcangle_it
1.648
2
616
X-RAY DIFFRACTION
r_scbond_it
2.804
3
256
X-RAY DIFFRACTION
r_scangle_it
3.97
4.5
205
LS refinement shell
Resolution: 2→2.05 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.231
16
-
Rwork
0.21
307
-
obs
-
323
79.75 %
Refinement TLS params.
Method: refined / Origin x: 39.585 Å / Origin y: 8.401 Å / Origin z: 9.051 Å
11
12
13
21
22
23
31
32
33
T
0.1078 Å2
-0.0109 Å2
0.0125 Å2
-
-0.0265 Å2
-0.0281 Å2
-
-
-0.0476 Å2
L
0.3283 °2
-0.7237 °2
0.0378 °2
-
3.4589 °2
0.9123 °2
-
-
0.5374 °2
S
0.0347 Å °
-0.001 Å °
0.0425 Å °
0.1228 Å °
-0.0734 Å °
0.0857 Å °
-0.0421 Å °
-0.0052 Å °
0.0387 Å °
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Auth asym-ID
Label asym-ID
Auth seq-ID
Label seq-ID
1
X-RAY DIFFRACTION
1
A
A
1 - 30
1 - 30
2
X-RAY DIFFRACTION
1
A
A
31 - 60
31 - 60
3
X-RAY DIFFRACTION
1
A
A
61 - 76
61 - 76
4
X-RAY DIFFRACTION
1
A
B
79 - 138
1 - 60
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