3KDD

Crystal Structure of HIV-1 Protease (Q7K, L33I, L63I) in Complex with KNI-10265


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1MSMPDB ENTRY 1MSM

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.2293citrate buffer pH 7.2, 100 mM DTT, 3mM NaN3 and 250 mM NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.754.38

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 58.408α = 90
b = 85.916β = 90
c = 46.438γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV2008-08-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU2001.54

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.841.386.10.06455.719350
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.81.86990.466.32193

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 1MSM1.841.31816699085.330.205890.203030.26178RANDOM27.55
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]
0.08-0.710.63
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.496
r_dihedral_angle_4_deg14.842
r_dihedral_angle_3_deg14.077
r_dihedral_angle_1_deg5.468
r_scangle_it1.936
r_angle_refined_deg1.347
r_scbond_it1.256
r_mcangle_it0.868
r_mcbond_it0.522
r_nbtor_refined0.306
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.496
r_dihedral_angle_4_deg14.842
r_dihedral_angle_3_deg14.077
r_dihedral_angle_1_deg5.468
r_scangle_it1.936
r_angle_refined_deg1.347
r_scbond_it1.256
r_mcangle_it0.868
r_mcbond_it0.522
r_nbtor_refined0.306
r_nbd_refined0.203
r_symmetry_hbond_refined0.181
r_symmetry_vdw_refined0.156
r_xyhbond_nbd_refined0.125
r_chiral_restr0.076
r_bond_refined_d0.009
r_gen_planes_refined0.003
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1516
Nucleic Acid Atoms
Solvent Atoms249
Heterogen Atoms57

Software

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