2AOG

Crystal structure analysis of HIV-1 protease mutant V82A with a substrate analog P2-NC


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2AODPDB Entry 2AOD

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.4293SODIUM CHLORIDE 0.4M, DMSO 5%,CITRATE PHOSPHATE BUFFER, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.6253

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 58.02α = 90
b = 85.893β = 90
c = 46.614γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray90CCDMARRESEARCH2003-09-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-ID0.92APS22-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.15094.80.10210.49.195318
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.11.1468.40.3772.12.6

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE RPDB Entry 2AOD1.1109016072253451294.90.12980.12790.166RANDOM
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
Coordinate Error
Structure Solution MethodRefinement High ResolutionRefinement Low Resolution
451652.11808.44
RMS Deviations
KeyRefinement Restraint Deviation
s_non_zero_chiral_vol0.098
s_approx_iso_adps0.093
s_zero_chiral_vol0.092
s_similar_adp_cmpnt0.053
s_anti_bump_dis_restr0.037
s_angle_d0.033
s_from_restr_planes0.0317
s_bond_d0.015
s_rigid_bond_adp_cmpnt0.005
s_similar_dist
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1508
Nucleic Acid Atoms
Solvent Atoms268
Heterogen Atoms89

Software

Software
Software NamePurpose
MAR345data collection
HKL-2000data reduction
SHELXmodel building
SHELXL-97refinement
HKL-2000data scaling
SHELXphasing