5VEA

HIV Protease (PR) with TL-3 in active site and 4-methylbenzene-1,2-diamine in exosite


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2AZ8 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.82980.5M KSCN, 0.1 M MES-HCl pH 5.8, 10% DMSO
Crystal Properties
Matthews coefficientSolvent content
2.1643.01

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 62.763α = 90
b = 62.763β = 90
c = 82.238γ = 120
Symmetry
Space GroupP 61 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2008-02-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL7-10.9794SSRLBL7-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym I (Observed)Rrim I (All)Rpim I (All)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
1232.7931000.0970.0970.1030.03314.69.46945
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Rrim I (All)Rpim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
122.051000.670.670.7090.22619.8

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 REPLACEMENTTHROUGHOUT2AZ8231.3965783281000.21780.21480.2799RANDOM33.439
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]
0.020.010.02-0.03
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg43.25
r_dihedral_angle_3_deg17.103
r_dihedral_angle_4_deg15.719
r_dihedral_angle_1_deg7.061
r_angle_refined_deg2.195
r_symmetry_vdw_refined0.357
r_nbtor_refined0.319
r_symmetry_hbond_refined0.296
r_nbd_refined0.277
r_xyhbond_nbd_refined0.23
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg43.25
r_dihedral_angle_3_deg17.103
r_dihedral_angle_4_deg15.719
r_dihedral_angle_1_deg7.061
r_angle_refined_deg2.195
r_symmetry_vdw_refined0.357
r_nbtor_refined0.319
r_symmetry_hbond_refined0.296
r_nbd_refined0.277
r_xyhbond_nbd_refined0.23
r_chiral_restr0.148
r_bond_refined_d0.027
r_gen_planes_refined0.008
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms759
Nucleic Acid Atoms
Solvent Atoms47
Heterogen Atoms54

Software

Software
Software NamePurpose
MOSFLMdata collection
SCALAdata scaling
MOLREPdata processing
REFMACrefinement
PDB_EXTRACTdata extraction
MOSFLMdata reduction
MOLREPphasing