3BVB

Cystal structure of HIV-1 Active Site Mutant D25N and inhibitor Darunavir


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1DAZPDB entry 1DAZ

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5295SODIUM ACETATE BUFFER, 30% SODIUM CHLORIDE, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
2.6854.15

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 58.26α = 90
b = 85.91β = 90
c = 46.051γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray95CCDMARRESEARCH2000-11-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-IDAPS22-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
11.35089.80.06217.54.9518724927842
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)
11.31.3571.80.62.23.1

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (I)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONAB INITIOFREE RPDB entry 1DAZ1.31025187249278259490.30.15990.150.21RANDOM
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
2216351697.8
RMS Deviations
KeyRefinement Restraint Deviation
s_non_zero_chiral_vol0.092
s_approx_iso_adps0.09
s_zero_chiral_vol0.065
s_similar_adp_cmpnt0.06
s_anti_bump_dis_restr0.038
s_angle_d0.033
s_from_restr_planes0.0291
s_bond_d0.013
s_rigid_bond_adp_cmpnt0.004
s_similar_dist
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1512
Nucleic Acid Atoms
Solvent Atoms196
Heterogen Atoms46

Software

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