Small outer capsid protein Soc / Small outer capsid protein / Small outer capsid protein superfamily / Small outer capsid protein / Outer Surface Protein A; domain 3 / Alpha-Beta Complex / Alpha Beta Similarity search - Domain/homology
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 1.54 Å / Relative weight: 1
Reflection
Resolution: 2.54→23.6 Å / Num. obs: 7033 / % possible obs: 99.6 % / Redundancy: 5.4 % / Rsym value: 0.058 / Net I/σ(I): 21.2
-
Processing
Software
Name
Version
Classification
MOLREP
phasing
PHENIX
(phenix.refine)
refinement
HKL-2000
datareduction
SCALEPACK
datascaling
Refinement
Method to determine structure: MOLECULAR REPLACEMENT Starting model: structure of the Soc protein from bacteriophage RB69 (hexagonal crystal form). Resolution: 2.254→23.595 Å / SU ML: 0.38 / σ(F): 1.35 / Stereochemistry target values: ML
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.2627
334
4.76 %
random
Rwork
0.2169
-
-
-
obs
0.2189
7023
99.67 %
-
Solvent computation
Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.408 Å2 / ksol: 0.316 e/Å3
Refinement step
Cycle: LAST / Resolution: 2.254→23.595 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
1168
0
10
120
1298
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
X-RAY DIFFRACTION
f_bond_d
0.002
1212
X-RAY DIFFRACTION
f_angle_d
0.421
1648
X-RAY DIFFRACTION
f_dihedral_angle_d
11.3
414
X-RAY DIFFRACTION
f_chiral_restr
0.03
178
X-RAY DIFFRACTION
f_plane_restr
0.003
214
LS refinement shell
Resolution (Å)
Rfactor Rfree
Num. reflection Rfree
Rfactor Rwork
Num. reflection Rwork
Refine-ID
% reflection obs (%)
2.2545-2.8396
0.3513
167
0.2559
3286
X-RAY DIFFRACTION
100
2.8396-23.5959
0.2235
167
0.1976
3403
X-RAY DIFFRACTION
100
Refinement TLS params.
Refine-ID: X-RAY DIFFRACTION
ID
Method
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
refined
2.2342
0.2625
0.8136
2.3718
1.1673
1.0355
0.2301
0.0658
-0.1947
-0.1277
-0.1324
-0.0603
0.4588
-0.1272
-0.087
0.2889
-0.0268
-0.0446
0.1479
-0.0119
0.1238
-8.34
40.8117
11.6614
2
2.6361
0.1321
-1.7101
0.5894
-0.2477
3.6751
0.5028
0.1481
0.3807
-0.1109
-0.1821
0.1512
-0.4247
-0.171
-0.3228
0.1872
-0.0161
0.0488
0.1095
0.0547
0.1249
Refinement TLS group
Selection details: chain B
+
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