3O9D

Crystal Structure of wild-type HIV-1 Protease in complex with kd19


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
2.0840.96

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 50.708α = 90
b = 57.6β = 90
c = 61.718γ = 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
11.855099.70.0612.1715998
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)
11.851.88970.3466.2

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 ?1.8539.191515679599.790.176570.174120.22613RANDOM29.054
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]
-0.66-0.330.99
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg42.621
r_dihedral_angle_4_deg13.598
r_dihedral_angle_3_deg11.865
r_dihedral_angle_1_deg6.274
r_scangle_it2.449
r_scbond_it1.626
r_angle_refined_deg1.372
r_mcangle_it1.078
r_angle_other_deg0.856
r_mcbond_it0.61
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg42.621
r_dihedral_angle_4_deg13.598
r_dihedral_angle_3_deg11.865
r_dihedral_angle_1_deg6.274
r_scangle_it2.449
r_scbond_it1.626
r_angle_refined_deg1.372
r_mcangle_it1.078
r_angle_other_deg0.856
r_mcbond_it0.61
r_mcbond_other0.154
r_chiral_restr0.081
r_bond_refined_d0.008
r_gen_planes_refined0.006
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 Atoms1480
Nucleic Acid Atoms
Solvent Atoms94
Heterogen Atoms59

Software

Software
Software NamePurpose
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
DENZOdata reduction
AMoREphasing