2O4L

Crystal Structure of HIV-1 Protease (Q7K, I50V) in Complex with Tipranavir


X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
Temperature 298.0
Details 0.75-1.5 M NaCl, 100 mM citrate buffer pH 5.4-6.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 58.96 α = 90
b = 86.41 β = 90
c = 46.19 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 ADSC QUANTUM 4 -- 2004-11-18
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON NSLS BEAMLINE X4A 1.008 NSLS X4A

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
1.33 24.35 85.0 0.077 0.077 -- 5.8 -- 46728 -- -- --
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)
1.33 1.38 88.5 0.397 0.397 5.62 5.1 4770

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 1.33 24.35 -- -- -- 46642 4719 84.99 -- 0.193 0.19 0.216 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 1.331 1.365 3465 355 3110 0.259 0.286 -- 86.91
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 16.639
Anisotropic B[1][1] -0.01
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.05
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.06
RMS Deviations
Key Refinement Restraint Deviation
r_nbd_refined 0.185
r_symmetry_vdw_refined 0.124
r_bond_refined_d 0.009
r_dihedral_angle_1_deg 5.678
r_xyhbond_nbd_refined 0.099
r_scbond_it 1.642
r_chiral_restr 0.081
r_gen_planes_refined 0.005
r_dihedral_angle_3_deg 10.939
r_angle_refined_deg 1.327
r_nbtor_refined 0.302
r_mcangle_it 1.045
r_dihedral_angle_4_deg 7.585
r_symmetry_hbond_refined 0.082
r_scangle_it 2.394
r_dihedral_angle_2_deg 41.99
r_mcbond_it 0.716
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1514
Nucleic Acid Atoms 0
Heterogen Atoms 56
Solvent Atoms 380

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
MOLREP phasing
REFMAC refinement
PDB_EXTRACT data extraction version: 2.000
HKL-2000 data reduction
HKL-2000 data scaling