6PRF

HIV-1 Protease multiple drug resistant clinical isolate mutant PR20 with GRL-14213A


X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 5.5
Temperature 298.0
Details 1.8 M sodium chloride, 0.1 M sodium acetate pH 5.5, 0.01M yittrium chloride

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 60.56 α = 90
b = 60.56 β = 90
c = 85.14 γ = 120
Symmetry
Space Group P 61

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
PIXEL DECTRIS EIGER X 16M -- 2018-10-25
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 22-ID 1 APS 22-ID

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
1.21 50 99.7 0.092 -- -- 7.5 -- 46059 -- -- 21.518
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)
1.21 1.25 90.0 0.5 -- 2.0 2.3 --

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 1.21 28.55 -- 0.0 -- 43734 2194 84.69 -- 0.154 0.1522 0.1897 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 1.21 1.239 -- 61 1403 0.315 0.281 0.0 36.55
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 21.518
Anisotropic B[1][1] -0.03
Anisotropic B[1][2] -0.02
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.03
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.11
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_1_deg 8.208
r_rigid_bond_restr 17.466
r_angle_refined_deg 2.179
r_chiral_restr 0.135
r_gen_planes_refined 0.015
r_dihedral_angle_2_deg 38.518
r_dihedral_angle_3_deg 14.988
r_bond_refined_d 0.015
r_dihedral_angle_4_deg 18.84
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1518
Nucleic Acid Atoms 0
Heterogen Atoms 105
Solvent Atoms 226

Software

Software
Software Name Purpose
HKL-2000 data reduction
HKL-2000 data scaling
PHASER phasing
REFMAC refinement version: 5.8.0238
PDB_EXTRACT data extraction version: 3.25