2QD8

HIV-1 Protease Mutant I84V with potent Antiviral inhibitor GRL-98065


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2Z4O 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP529825mM sodium acetate, 8% (w/v) sodium chloride, 10% (v/v) dimethylsulfoxide (DMSO), pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.754.39

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 58.423α = 90
b = 86.182β = 90
c = 45.986γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mm2002-12-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-ID1.000APS22-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
11.355098.50.05117.39.8524655190313.4
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)
1.351.486.60.3084.655.24430

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 REPLACEMENTTHROUGHOUT2Z4O1.35105095450838253598.50.13270.13040.1752RANDOM
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
2916271742.69
RMS Deviations
KeyRefinement Restraint Deviation
s_approx_iso_adps0.092
s_non_zero_chiral_vol0.084
s_zero_chiral_vol0.066
s_similar_adp_cmpnt0.036
s_angle_d0.032
s_from_restr_planes0.0291
s_anti_bump_dis_restr0.021
s_bond_d0.012
s_rigid_bond_adp_cmpnt0.004
s_similar_dist
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1632
Nucleic Acid Atoms
Solvent Atoms224
Heterogen Atoms91

Software

Software
Software NamePurpose
AMoREphasing
SHELXL-97refinement
MAR345data collection
HKL-2000data reduction
HKL-2000data scaling