6AY9

Structure of the native full-length HIV-1 capsid protein in complex with CPSF6 peptide


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 = 92.68 α = 90
b = 92.68 β = 90
c = 58.04 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 EIGER X 16M -- 2017-03-14
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 23-ID-B 1.033203 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
2.5 47.03 99.9 0.063 -- -- 5.6 -- 9956 -- -- 60.78
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)
2.5 2.6 100.0 0.7 -- -- 5.5 --

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 2.5 47.03 -- 1.39 -- 9950 598 99.83 -- 0.2438 0.2421 0.2727 --
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 2.5002 2.7518 -- 167 2295 0.3561 0.3732 0.0 100.0
X Ray Diffraction 2.7518 3.1499 -- 181 2284 0.2913 0.3217 0.0 100.0
X Ray Diffraction 3.1499 3.9682 -- 123 2356 0.2359 0.2606 0.0 100.0
X Ray Diffraction 3.9682 47.0403 -- 127 2417 0.2164 0.2391 0.0 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 75.0984
RMS Deviations
Key Refinement Restraint Deviation
f_angle_d 0.496
f_plane_restr 0.004
f_dihedral_angle_d 13.353
f_bond_d 0.002
f_chiral_restr 0.038
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1791
Nucleic Acid Atoms 0
Heterogen Atoms 10
Solvent Atoms 31

Software

Software
Software Name Purpose
Aimless data scaling version: 0.5.32
Blu-Ice data collection
PHENIX refinement version: 1.11.1-2575_1692
PDB_EXTRACT data extraction version: 3.22
Aimless data reduction version: 0.5.32
PHASER phasing version: 2.7.17