3KDB

Crystal Structure of HIV-1 Protease (Q7K, L33I, L63I) in Complex with KNI-10006


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.2293citrate buffer pH 6.2, NaCl 500 mM, 100 mM DTT, 3mM NaN3, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.7254.75

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 58.627α = 90
b = 85.907β = 90
c = 46.652γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV2007-04-14MSINGLE 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
11.6648.4585.90.0645.65.124519
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)
11.661.721000.463.94.92793

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 1MSM1.6648.4523172124285.640.21410.212040.25502RANDOM25.863
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]
0.19-0.850.66
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.992
r_dihedral_angle_3_deg13.063
r_dihedral_angle_4_deg11.235
r_dihedral_angle_1_deg5.665
r_scangle_it2.902
r_scbond_it1.97
r_angle_refined_deg1.566
r_mcangle_it1.272
r_mcbond_it0.843
r_nbtor_refined0.307
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.992
r_dihedral_angle_3_deg13.063
r_dihedral_angle_4_deg11.235
r_dihedral_angle_1_deg5.665
r_scangle_it2.902
r_scbond_it1.97
r_angle_refined_deg1.566
r_mcangle_it1.272
r_mcbond_it0.843
r_nbtor_refined0.307
r_nbd_refined0.215
r_symmetry_vdw_refined0.162
r_xyhbond_nbd_refined0.142
r_symmetry_hbond_refined0.138
r_chiral_restr0.092
r_bond_refined_d0.012
r_gen_planes_refined0.005
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 Atoms233
Heterogen Atoms51

Software

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