5JPA

Hexameric HIV-1 CA H12Y mutant


X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 8
Temperature 290.0
Details PEG 550MME (12% w/v), KSCN (0.15M), 0.1M TRIS

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 90.6 α = 90
b = 90.6 β = 90
c = 56.93 γ = 120
Symmetry
Space Group P 6

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
PIXEL DECTRIS PILATUS 6M-F -- 2014-12-01
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON DIAMOND BEAMLINE I02 0.9794 Diamond I02

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
1.7 56.93 95.1 0.095 -- -- 4.8 -- 27756 -- -- --
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)
1.7 1.73 94.7 0.813 -- -- 4.9 --

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 1.7 56.93 -- 0.0 -- 26370 1379 94.27 -- 0.199 0.1971 0.232 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 1.7 1.744 -- 81 1949 0.265 0.285 -- 93.59
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 27.491
Anisotropic B[1][1] 0.24
Anisotropic B[1][2] 0.12
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.24
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.79
RMS Deviations
Key Refinement Restraint Deviation
r_mcbond_it 2.194
r_dihedral_angle_4_deg 18.225
r_gen_planes_other 0.001
r_angle_refined_deg 1.009
r_mcbond_other 2.184
r_bond_other_d 0.001
r_gen_planes_refined 0.004
r_dihedral_angle_2_deg 31.619
r_chiral_restr 0.06
r_bond_refined_d 0.006
r_dihedral_angle_3_deg 11.5
r_mcangle_it 3.405
r_angle_other_deg 0.843
r_dihedral_angle_1_deg 4.83
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1609
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 123

Software

Software
Software Name Purpose
Aimless data scaling version: 0.4.10
PHASER phasing version: 2.5.6
REFMAC refinement version: 5.8.0135
PDB_EXTRACT data extraction version: 3.20
iMOSFLM data reduction version: 7.2.1