2J9J

Atomic-resolution Crystal Structure of Chemically-Synthesized HIV-1 Protease Complexed with Inhibitor JG-365


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 7HVPPDB ENTRY 7HVP

Crystallization

Crystal Properties
Matthews coefficientSolvent content
1.6625.22

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 50.548α = 90
b = 58.814β = 90
c = 60.889γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray150 MSINGLE WAVELENGTH
21x-ray MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 14-BM-CAPS14-BM-C
2SYNCHROTRONAPS BEAMLINE 19-BMAPS19-BM

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
11.045093.80.063310.182488
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)
11.041.0882.20.4223.2

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUEPDB ENTRY 7HVP1.041073981823784.50.1310.1420.191RANDOM
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
321665.21950.7
RMS Deviations
KeyRefinement Restraint Deviation
s_zero_chiral_vol0.12
s_approx_iso_adps0.108
s_non_zero_chiral_vol0.103
s_anti_bump_dis_restr0.065
s_similar_adp_cmpnt0.043
s_angle_d0.041
s_from_restr_planes0.034
s_bond_d0.019
s_rigid_bond_adp_cmpnt0.006
s_similar_dist
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1570
Nucleic Acid Atoms
Solvent Atoms240
Heterogen Atoms31

Software

Software
Software NamePurpose
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing