1ZPK

Crystal structure of the complex of mutant HIV-1 protease (A71V, V82T, I84V) with a hydroxyethylamine peptidomimetic inhibitor BOC-PHE-PSI[R-CH(OH)CH2NH]-PHE-GLU-PHE-NH2


X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Microseeding
pH 4.4
Temperature 298.0
Details 0.5 M NaCl, 0.1 M Na Citrate, 10% Glycerol, pH 4.4, microseeding, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 62.48 α = 90
b = 62.48 β = 90
c = 82.41 γ = 120
Symmetry
Space Group P 61

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARRESEARCH microfocusing mirrors - testing 2000-04-12
Diffraction Radiation
Monochromator Protocol
Diamond C 111 SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID14-1 0.934 ESRF ID14-1

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 30 99.9 0.039 0.039 -- 6.9 21955 21955 -- -999.0 24.9
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 1.69 99.8 0.37 0.37 2.3 3.0 1464

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 1.65 10.0 -- 0.0 21836 21836 1090 99.9 0.1586 0.1586 0.1559 0.2528 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 1.65 1.69 1503 -- -- 0.306 -- -- --
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model anisotropic
Mean Isotropic B 41.4
RMS Deviations
Key Refinement Restraint Deviation
s_approx_iso_adps 0.0
s_from_restr_planes 0.0257
s_non_zero_chiral_vol 0.043
s_similar_dist 0.047
s_anti_bump_dis_restr 0.007
s_angle_d 0.026
s_similar_adp_cmpnt 0.072
s_rigid_bond_adp_cmpnt 0.002
s_bond_d 0.007
s_zero_chiral_vol 0.037
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.13
Number Disordered Residues 21.0
Occupancy Sum Hydrogen 1645.0
Occupancy Sum Non Hydrogen 1701.5
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1526
Nucleic Acid Atoms 0
Heterogen Atoms 53
Solvent Atoms 160

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
AMoRE phasing
SHELXL-97 refinement