4J5J

Crystal Structure of Multidrug Resistant HIV-1 Protease Clinical Isolate PR20 in Complex with Amprenavir


X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 4.2
Temperature 298.0
Details 1.67 M sodium chloride, 67 mM citrate/phosphate, pH 4.2, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 28.72 α = 90
b = 65.8 β = 90
c = 93.56 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 MARMOSAIC 225 mm CCD mirrors 2009-08-13
Diffraction Radiation
Monochromator Protocol
Rosenbaum-Rock double-crystal Si(220) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 22-BM 0.84999 APS 22-BM

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 50 97.6 0.073 -- -- 4.5 17214 16791 2.0 2.0 --
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 1.86 80.0 0.468 -- 2.1 3.1 --

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 1.8 9.91 -- -- 17214 15764 828 97.65 -- 0.19015 0.18743 0.24279 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 1.8 1.845 -- 53 868 0.255 0.357 -- 77.98
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 24.471
Anisotropic B[1][1] 0.2
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] -0.15
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_1_deg 7.02
r_scbond_it 3.199
r_symmetry_hbond_refined 0.083
r_dihedral_angle_3_deg 14.446
r_dihedral_angle_4_deg 10.208
r_symmetry_vdw_refined 0.168
r_angle_refined_deg 2.108
r_chiral_restr 0.156
r_mcbond_it 1.427
r_xyhbond_nbd_refined 0.104
r_scangle_it 5.18
r_bond_refined_d 0.024
r_gen_planes_refined 0.01
r_nbtor_refined 0.311
r_dihedral_angle_2_deg 38.889
r_nbd_refined 0.209
r_mcangle_it 2.394
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1518
Nucleic Acid Atoms 0
Heterogen Atoms 73
Solvent Atoms 95

Software

Software
Software Name Purpose
SERGUI data collection
MOLREP phasing
REFMAC refinement version: 5.2.0019
HKL-2000 data reduction
HKL-2000 data scaling