3O9A

Crystal Structure of wild-type HIV-1 Protease in complex with kd14


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
2.141.31

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 50.745α = 90
b = 57.751β = 90
c = 61.876γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV2008-06-24SINGLE 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
11.95099.90.08810.26.814888
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)
11.91.9799.90.3876

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 ?1.942.221409575299.840.181060.179180.21551RANDOM22.212
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]
-1.150.210.94
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg42.341
r_dihedral_angle_4_deg19.889
r_dihedral_angle_3_deg12.135
r_dihedral_angle_1_deg6.054
r_scangle_it1.699
r_angle_refined_deg1.273
r_scbond_it1.173
r_angle_other_deg0.812
r_mcangle_it0.756
r_mcbond_it0.52
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg42.341
r_dihedral_angle_4_deg19.889
r_dihedral_angle_3_deg12.135
r_dihedral_angle_1_deg6.054
r_scangle_it1.699
r_angle_refined_deg1.273
r_scbond_it1.173
r_angle_other_deg0.812
r_mcangle_it0.756
r_mcbond_it0.52
r_symmetry_vdw_other0.218
r_symmetry_vdw_refined0.207
r_nbd_other0.191
r_nbd_refined0.173
r_nbtor_refined0.166
r_xyhbond_nbd_refined0.127
r_symmetry_hbond_refined0.122
r_mcbond_other0.113
r_nbtor_other0.084
r_chiral_restr0.077
r_bond_refined_d0.009
r_gen_planes_refined0.003
r_bond_other_d0.002
r_gen_planes_other0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
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 Atoms1486
Nucleic Acid Atoms
Solvent Atoms113
Heterogen Atoms60

Software

Software
Software NamePurpose
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
DENZOdata reduction
AMoREphasing