6B2G

P38A mutant of HIV-1 capsid protein


X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
Temperature 291.0
Details PEG3350, NaI, MIB, Glycerol

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 92.14 α = 90
b = 92.14 β = 90
c = 57.48 γ = 120
Symmetry
Space Group P 6

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 300 mm CCD -- 2016-04-10
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 23-ID-B 1.033200 APS 23-ID-B

Data Collection

Overall
Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot
2.41 46.64 99.6 0.065 -- -- 10.1 -- 10898 -- -- 69.59
High Resolution Shell
Resolution (High) Resolution (Low) Percent Possible (All) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All)
2.41 2.5 96.7 1.038 -- -- 9.6 --

Refinement

Statistics
Structure Solution Method Refinement High Resolution Refinement Low Resolution Cut-off Sigma (I) Cut-off Sigma (F) Number of Reflections (All) Number of Reflections (Observed) Number of Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work R-Free R-Free Selection Details
MOLECULAR REPLACEMENT 2.407 46.64 -- 1.39 -- 10894 631 99.7 -- 0.2391 0.238 0.2578 --
High Resolution Shell
Refinement method Shell Resolution (High) Shell Resolution (Low) # of Reflections (Observed) # of Reflections (R-Free) # of Reflections (R-Work) R-Factor (R-Work) R-Factor (R-Free) R-Factor (R-Free Error) Percent Reflections (Observed)
X Ray Diffraction 2.4068 2.5926 -- 115 2013 0.3567 0.3794 0.0 99.0
X Ray Diffraction 2.5926 2.8535 -- 125 2038 0.3403 0.3844 0.0 100.0
X Ray Diffraction 2.8535 3.2663 -- 133 2039 0.3084 0.3228 0.0 100.0
X Ray Diffraction 3.2663 4.1148 -- 122 2065 0.2475 0.2325 0.0 100.0
X Ray Diffraction 4.1148 46.6486 -- 136 2108 0.1944 0.2281 0.0 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 93.4195
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 12.06
f_plane_restr 0.004
f_angle_d 0.447
f_bond_d 0.002
f_chiral_restr 0.037
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1696
Nucleic Acid Atoms 0
Heterogen Atoms 13
Solvent Atoms 33

Software

Software
Software Name Purpose
Aimless data scaling version: 0.5.31
Blu-Ice data collection
PHENIX refinement version: 1.11.1-2575_1692
PDB_EXTRACT data extraction version: 3.22
Aimless data reduction version: 0.5.31
PHASER phasing version: 2.7.17