3MXD

Crystal structure of HIV-1 protease inhibitor KC53 in complex with wild-type protease


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16.2298126 mM sodium phosphate pH 6.2, 63 mM sodium citrate, 24-29% ammonium sulphate, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.141.37

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 50.674α = 90
b = 57.858β = 90
c = 61.914γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray200IMAGE PLATERIGAKU RAXIS IVOSMIC MIRRORS2007-03-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU

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
11.955099.70.1020.1028.36.613809

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1F7A1.9539.22130801308068999.570.166770.164970.20087RANDOM21.641
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]
-0.390.210.18
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.759
r_dihedral_angle_4_deg19.619
r_dihedral_angle_3_deg11.223
r_dihedral_angle_1_deg6.05
r_scangle_it1.509
r_angle_refined_deg1.34
r_scbond_it1.015
r_angle_other_deg0.711
r_mcangle_it0.71
r_mcbond_it0.494
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.759
r_dihedral_angle_4_deg19.619
r_dihedral_angle_3_deg11.223
r_dihedral_angle_1_deg6.05
r_scangle_it1.509
r_angle_refined_deg1.34
r_scbond_it1.015
r_angle_other_deg0.711
r_mcangle_it0.71
r_mcbond_it0.494
r_symmetry_vdw_other0.195
r_nbd_other0.18
r_nbd_refined0.178
r_nbtor_refined0.166
r_symmetry_vdw_refined0.146
r_xyhbond_nbd_refined0.134
r_symmetry_hbond_refined0.119
r_mcbond_other0.103
r_nbtor_other0.081
r_chiral_restr0.071
r_bond_refined_d0.008
r_gen_planes_refined0.003
r_bond_other_d0.001
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 Atoms1486
Nucleic Acid Atoms
Solvent Atoms114
Heterogen Atoms68

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing