3O9G

Crystal Structure of wild-type HIV-1 Protease in complex with af53


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1hanging drop, vapor diffusion6.2295126mM Phosphate buffer pH 6.2, 63mM Sodium Citrate, 24-29% Ammonium Sulfate, hanging drop, vapor diffusion, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
2.0941.16

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 50.675α = 90
b = 57.816β = 90
c = 61.741γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV2009-02-20SINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU1.5418

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
11.655099.20.043166.622322
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)
11.651.7194.10.3715.4

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 entry1.6542.2221130114299.070.177380.175940.20339RANDOM26.925
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]
-0.820.320.49
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.448
r_dihedral_angle_4_deg13.12
r_dihedral_angle_3_deg11.51
r_dihedral_angle_1_deg6.017
r_scangle_it2.483
r_scbond_it1.62
r_angle_refined_deg1.402
r_mcangle_it0.995
r_angle_other_deg0.844
r_mcbond_it0.581
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.448
r_dihedral_angle_4_deg13.12
r_dihedral_angle_3_deg11.51
r_dihedral_angle_1_deg6.017
r_scangle_it2.483
r_scbond_it1.62
r_angle_refined_deg1.402
r_mcangle_it0.995
r_angle_other_deg0.844
r_mcbond_it0.581
r_mcbond_other0.172
r_chiral_restr0.095
r_bond_refined_d0.008
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1490
Nucleic Acid Atoms
Solvent Atoms136
Heterogen Atoms56

Software

Software
Software NamePurpose
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
DENZOdata reduction
AMoREphasing