6AXY

Structure of the V11I/T58A/I124A mutant of the 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, Sodium cacodylate, Glycerol

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 91.92 α = 90
b = 91.92 β = 90
c = 57.92 γ = 120
Symmetry
Space Group P 6

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CMOS RDI CMOS_8M -- 2016-12-01
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ALS BEAMLINE 4.2.2 1.000031 ALS 4.2.2

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
2.78 45.96 97.3 0.109 -- -- 10.6 -- 6969 -- -- --
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)
2.78 2.93 97.3 1.05 -- -- 9.9 --

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 2.78 45.96 -- 0.0 -- 6576 383 97.14 -- 0.2156 0.2131 0.26 RANDOM
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 2.777 2.849 -- 18 472 0.368 0.554 0.0 95.15
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 74.506
Anisotropic B[1][1] -0.39
Anisotropic B[1][2] -0.19
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.39
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 1.26
RMS Deviations
Key Refinement Restraint Deviation
r_bond_other_d 0.001
r_angle_other_deg 0.852
r_dihedral_angle_4_deg 18.695
r_chiral_restr 0.054
r_dihedral_angle_3_deg 12.558
r_dihedral_angle_1_deg 5.467
r_bond_refined_d 0.007
r_gen_planes_other 0.001
r_dihedral_angle_2_deg 34.873
r_gen_planes_refined 0.004
r_angle_refined_deg 1.085
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1680
Nucleic Acid Atoms 0
Heterogen Atoms 16
Solvent Atoms 30

Software

Software
Software Name Purpose
Aimless data scaling version: 0.5.32
Blu-Ice data collection
REFMAC refinement version: 5.8.0158
PDB_EXTRACT data extraction version: 3.22
Aimless data reduction version: 0.5.32
PHASER phasing version: 2.7.17