3O9B

Crystal Structure of wild-type HIV-1 Protease in Complex with kd25


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
2.0941.27

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 50.672α = 90
b = 57.921β = 90
c = 61.746γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152009-04-16SINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 14-BM-C0.9APS14-BM-C

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
11.55099.80.06711.77.829830
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)
11.51.551000.3687.9

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 ?1.542.2628263150899.820.166370.165210.18898RANDOM11.433
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]
-0.630.210.41
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg42.284
r_dihedral_angle_4_deg11.586
r_dihedral_angle_3_deg11.354
r_dihedral_angle_1_deg6.135
r_scangle_it2.332
r_scbond_it1.499
r_angle_refined_deg1.266
r_mcangle_it0.92
r_angle_other_deg0.778
r_mcbond_it0.489
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg42.284
r_dihedral_angle_4_deg11.586
r_dihedral_angle_3_deg11.354
r_dihedral_angle_1_deg6.135
r_scangle_it2.332
r_scbond_it1.499
r_angle_refined_deg1.266
r_mcangle_it0.92
r_angle_other_deg0.778
r_mcbond_it0.489
r_mcbond_other0.11
r_chiral_restr0.08
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 Atoms1498
Nucleic Acid Atoms
Solvent Atoms168
Heterogen Atoms69

Software

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