2Q54

Crystal structure of KB73 bound to HIV-1 protease


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.2298126 mM sodium phosphate, 63 mM sodium citrate, 24-29% ammonium sulphate, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.0941.29

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 50.759α = 90
b = 58.167β = 90
c = 61.436γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray200IMAGE PLATERIGAKU RAXIS IVosmic mirrors2006-09-08MSINGLE 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)R Sym 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
11.855095.50.0383.819.76.615398

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 1F7A1.8542.221459676995.620.176510.174120.22399RANDOM23.911
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]
-0.6-0.390.99
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.503
r_dihedral_angle_4_deg14.8
r_dihedral_angle_3_deg11.558
r_dihedral_angle_1_deg6.05
r_scangle_it1.527
r_angle_refined_deg1.207
r_scbond_it1.01
r_mcangle_it0.719
r_angle_other_deg0.685
r_mcbond_it0.479
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.503
r_dihedral_angle_4_deg14.8
r_dihedral_angle_3_deg11.558
r_dihedral_angle_1_deg6.05
r_scangle_it1.527
r_angle_refined_deg1.207
r_scbond_it1.01
r_mcangle_it0.719
r_angle_other_deg0.685
r_mcbond_it0.479
r_symmetry_vdw_other0.197
r_nbd_other0.179
r_nbd_refined0.174
r_nbtor_refined0.165
r_symmetry_vdw_refined0.165
r_xyhbond_nbd_refined0.13
r_symmetry_hbond_refined0.108
r_mcbond_other0.102
r_nbtor_other0.08
r_chiral_restr0.065
r_bond_refined_d0.008
r_gen_planes_refined0.003
r_bond_other_d0.002
r_gen_planes_other0.002
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 Atoms135
Heterogen Atoms66

Software

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