3QIH

HIV-1 protease (mutant Q7K L33I L63I) in complex with a novel inhibitor


X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 5.5
Temperature 289.0
Details 500mM NaCl, 100mM Na citrate, 100mM DTT, 3mM NaN3, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 58.04 α = 90
b = 85.42 β = 90
c = 46.71 γ = 90
Symmetry
Space Group P 21 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD RAYONIX MX-225 mirrors 2010-12-15
Diffraction Radiation
Monochromator Protocol
Double Crystal Monochromator KMC-2 SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON BESSY BEAMLINE 14.2 0.91841 BESSY 14.2

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
1.39 50 100.0 -- 0.066 -- 4.4 47014 47014 -- -- 13.72
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)
1.39 1.41 100.0 -- 0.471 3.0 4.2 2342

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 1.39 24.005 -- 0.0 44810 44810 2243 94.34 -- 0.1523 0.1512 0.1709 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 1.39 1.4397 -- 203 3847 0.1932 0.2498 -- 87.0
X Ray Diffraction 1.4397 1.4973 -- 242 3977 0.1721 0.1881 -- 90.0
X Ray Diffraction 1.4973 1.5655 -- 204 4143 0.1339 0.1685 -- 92.0
X Ray Diffraction 1.5655 1.648 -- 218 4237 0.1164 0.1545 -- 95.0
X Ray Diffraction 1.648 1.7512 -- 218 4292 0.1135 0.155 -- 96.0
X Ray Diffraction 1.7512 1.8863 -- 220 4307 0.1207 0.1516 -- 96.0
X Ray Diffraction 1.8863 2.0761 -- 238 4472 0.126 0.1632 -- 99.0
X Ray Diffraction 2.0761 2.3763 -- 230 4486 0.1426 0.1592 -- 100.0
X Ray Diffraction 2.3763 2.9929 -- 242 4537 0.1642 0.1811 -- 99.0
X Ray Diffraction 2.9929 24.0087 -- 228 4269 0.1725 0.1744 -- 90.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 21.213
Anisotropic B[1][1] 5.3665
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -3.8507
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.5159
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.006
f_angle_d 1.209
f_chiral_restr 0.065
f_dihedral_angle_d 15.946
f_bond_d 0.006
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1506
Nucleic Acid Atoms 0
Heterogen Atoms 64
Solvent Atoms 280

Software

Software
Software Name Purpose
MAR345dtb data collection
PHASER phasing
PHENIX refinement version: (phenix.refine: 1.6.4_486)
HKL-2000 data reduction
HKL-2000 data scaling