3KT5

Crystal Structure of N88S mutant HIV-1 Protease


X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.2
Temperature 298.0
Details 1-5% saturated Ammonium Sulfate, 200/100mM Phosphate/Citrate Buffer, pH 6.2, vapor diffusion, hanging drop, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 62.17 α = 90
b = 62.17 β = 90
c = 83 γ = 120
Symmetry
Space Group P 61

Diffraction

Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315r -- 2009-03-12
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID29 0.976180 ESRF ID29

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
1.8 32.87 99.6 0.067 -- -- 5.4 16879 16807 0.0 0.0 20.85
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)
1.8 1.91 99.0 0.537 -- -- 5.45 2695

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
FOURIER SYNTHESIS 1.801 32.869 -- 2.0 -- 16801 841 99.56 -- 0.18 0.178 0.225 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 1.801 1.914 -- 140 2655 0.223 0.263 -- 99.0
X Ray Diffraction 1.914 2.062 -- 139 2647 0.208 0.279 -- 100.0
X Ray Diffraction 2.062 2.269 -- 140 2652 0.199 0.275 -- 100.0
X Ray Diffraction 2.269 2.598 -- 141 2677 0.191 0.209 -- 100.0
X Ray Diffraction 2.598 3.272 -- 140 2663 0.175 0.225 -- 100.0
X Ray Diffraction 3.272 32.875 -- 141 2666 0.152 0.194 -- 99.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 29.353
Anisotropic B[1][1] 0.314
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.314
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.628
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.007
f_bond_d 0.007
f_chiral_restr 0.074
f_dihedral_angle_d 18.67
f_angle_d 1.118
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1588
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 241

Software

Software
Software Name Purpose
PHENIX refinement
PDB_EXTRACT data extraction version: 3.005
ADSC data collection version: Quantum
XDS data reduction
XDS data scaling
PHENIX phasing