6ECO

Hexamer-2-Foldon HIV-1 capsid platform


X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Microbatch
pH 7.5
Temperature 293.0
Details 0.2M Sodium Chloride, 0.1M HEPES pH 7.5, 12% PEG 8000

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 95.25 α = 90
b = 95.25 β = 90
c = 122.57 γ = 120
Symmetry
Space Group P 3 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
PIXEL DECTRIS EIGER X 9M -- 2017-05-25
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON NSLS-II BEAMLINE 17-ID-1 0.9798 NSLS-II 17-ID-1

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
4.2 50.01 94.7 0.11 -- -- 3.0 -- 8601 -- -- --
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)
4.2 4.31 -- 0.9 -- 1.4 -- --

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 4.2 30.0 -- -- -- 4690 214 98.14 -- 0.28766 0.28637 0.31638 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 4.2 4.307 -- 15 327 0.475 0.367 -- 97.71
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 256.555
Anisotropic B[1][1] -12.68
Anisotropic B[1][2] -6.34
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -12.68
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 41.15
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_2_deg 33.166
r_angle_refined_deg 1.349
r_dihedral_angle_3_deg 11.464
r_dihedral_angle_4_deg 15.074
r_gen_planes_refined 0.009
r_chiral_restr 0.096
r_dihedral_angle_1_deg 4.601
r_bond_refined_d 0.012
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3252
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 0

Software

Software
Software Name Purpose
REFMAC refinement version: 5.8.0103
XDS data scaling version: 20180126
XDS data reduction version: 20180126
PHASER phasing version: 7.0.0
Coot model building version: 0.8.7