4F75

Crystal Structure of active HIV-1 Protease in Complex with the N terminal product of the substrate RH-IN


X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.2
Temperature 295.0
Details 126mM Phosphate buffer pH 6.2, 63mM Sodium Citrate, 24-31% Ammonium Sulfate, hanging drop, vapor diffusion, temperature 295K, VAPOR DIFFUSION, HANGING DROP

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 50.78 α = 90
b = 58.11 β = 90
c = 61.8 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315 -- 2010-07-15
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 14-BM-C 0.9 APS 14-BM-C

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
1.65 50 99.7 0.058 -- -- 7.8 -- 22603 -- -- --
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)
1.65 1.71 99.7 0.525 -- -- 7.9 2219

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 42.33 -- 0.0 -- 20581 1053 99.35 -- 0.1711 0.1699 0.1934 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 -- 58 1423 0.196 0.215 -- 99.53
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 23.0717
Anisotropic B[1][1] -1.0
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.11
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 1.11
RMS Deviations
Key Refinement Restraint Deviation
r_gen_planes_other 0.002
r_dihedral_angle_3_deg 12.19
r_angle_refined_deg 1.344
r_bond_other_d 0.001
r_bond_refined_d 0.009
r_mcbond_it 0.581
r_mcbond_other 0.177
r_scangle_it 2.651
r_angle_other_deg 0.835
r_dihedral_angle_4_deg 16.06
r_gen_planes_refined 0.006
r_mcangle_it 0.973
r_chiral_restr 0.086
r_dihedral_angle_1_deg 6.434
r_dihedral_angle_2_deg 38.606
r_scbond_it 1.676
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1540
Nucleic Acid Atoms 0
Heterogen Atoms 10
Solvent Atoms 120

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
REFMAC refinement
PDB_EXTRACT data extraction version: 3.11