6AXX

Structure of the 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, MIB, Glycerol

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 91.65 α = 90
b = 91.65 β = 90
c = 57.69 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
2.6 45.82 99.5 0.107 -- -- 10.6 -- 8617 -- -- --
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)
2.6 2.71 96.0 1.391 -- -- 9.7 --

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 2.6 45.8 -- 0.0 -- 8101 512 99.68 -- 0.1931 0.1896 0.2465 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 2.6 2.667 -- 38 559 0.325 0.299 0.0 96.92
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 69.192
Anisotropic B[1][1] -0.02
Anisotropic B[1][2] -0.01
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.02
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.05
RMS Deviations
Key Refinement Restraint Deviation
r_bond_refined_d 0.009
r_gen_planes_refined 0.005
r_chiral_restr 0.061
r_angle_other_deg 0.931
r_dihedral_angle_3_deg 13.513
r_dihedral_angle_1_deg 5.899
r_dihedral_angle_4_deg 17.618
r_bond_other_d 0.002
r_sphericity_bonded 32.167
r_angle_refined_deg 1.315
r_gen_planes_other 0.001
r_sphericity_free 33.13
r_dihedral_angle_2_deg 33.979
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1658
Nucleic Acid Atoms 0
Heterogen Atoms 17
Solvent Atoms 48

Software

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