3SA3

Crystal structure of wild-type HIV-1 protease in complex with AG23


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1F7APDB ENTRY 1F7A

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1HANGING DROP, VAPOR DIFFUSION6.229524-29% ammonium sulfate, 63 mM sodium citrate, 126 mM phosphate buffer, pH 6.2, HANGING DROP, VAPOR DIFFUSION, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
2.0439.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 50.386α = 90
b = 57.33β = 90
c = 61.097γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152010-01-20SINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X29ANSLSX29A

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
11.655096.50.05713.24.921177
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)
11.651.7197.20.3564.82089

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1F7A1.6541.8121153108096.560.17370.17220.203RANDOM25.181
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]
-1.09-0.31.39
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.586
r_dihedral_angle_4_deg14.748
r_dihedral_angle_3_deg12.829
r_dihedral_angle_1_deg6.584
r_scangle_it2.732
r_scbond_it1.846
r_angle_refined_deg1.434
r_mcangle_it1.065
r_angle_other_deg0.826
r_mcbond_it0.609
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.586
r_dihedral_angle_4_deg14.748
r_dihedral_angle_3_deg12.829
r_dihedral_angle_1_deg6.584
r_scangle_it2.732
r_scbond_it1.846
r_angle_refined_deg1.434
r_mcangle_it1.065
r_angle_other_deg0.826
r_mcbond_it0.609
r_mcbond_other0.16
r_chiral_restr0.087
r_bond_refined_d0.009
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1494
Nucleic Acid Atoms
Solvent Atoms126
Heterogen Atoms58

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
AMoREphasing