2Q55

Crystal structure of KK44 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
2.1342.16

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 50.844α = 90
b = 58.53β = 90
c = 61.869γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray200IMAGE PLATERIGAKU RAXIS IVosmic mirrors2006-08-24MSINGLE 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
11.95099.70.0545.410.16.315088

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 1F7A1.942.521429075799.470.177630.174810.23473RANDOM17.713
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]
-0.530.020.51
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.652
r_dihedral_angle_4_deg14.199
r_dihedral_angle_3_deg10.886
r_dihedral_angle_1_deg6.314
r_scangle_it1.782
r_angle_refined_deg1.292
r_scbond_it1.211
r_mcangle_it0.741
r_angle_other_deg0.697
r_mcbond_it0.51
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.652
r_dihedral_angle_4_deg14.199
r_dihedral_angle_3_deg10.886
r_dihedral_angle_1_deg6.314
r_scangle_it1.782
r_angle_refined_deg1.292
r_scbond_it1.211
r_mcangle_it0.741
r_angle_other_deg0.697
r_mcbond_it0.51
r_symmetry_vdw_other0.18
r_nbd_other0.176
r_nbd_refined0.174
r_nbtor_refined0.167
r_xyhbond_nbd_refined0.143
r_mcbond_other0.113
r_symmetry_vdw_refined0.112
r_symmetry_hbond_refined0.11
r_chiral_restr0.084
r_nbtor_other0.079
r_bond_refined_d0.009
r_gen_planes_refined0.004
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 Atoms1498
Nucleic Acid Atoms
Solvent Atoms136
Heterogen Atoms58

Software

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