2QI0

Crystal structure of protease inhibitor, MIT-1-KK80 in complex with wild type 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
2.1241.86

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 50.975α = 90
b = 58.242β = 90
c = 61.701γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray200IMAGE PLATERIGAKU RAXIS IVosmic mirrors2006-02-23MSINGLE 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
12.150990.0515.110.76.911126

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTpdb entry 1F7A2.142.371056353099.030.173070.173070.170340.2302RANDOM30.983
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]
-0.710.170.53
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.691
r_dihedral_angle_3_deg13.17
r_dihedral_angle_4_deg13.139
r_dihedral_angle_1_deg6.855
r_scangle_it2.534
r_scbond_it1.626
r_angle_refined_deg1.267
r_mcangle_it1.018
r_mcbond_it0.718
r_angle_other_deg0.65
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.691
r_dihedral_angle_3_deg13.17
r_dihedral_angle_4_deg13.139
r_dihedral_angle_1_deg6.855
r_scangle_it2.534
r_scbond_it1.626
r_angle_refined_deg1.267
r_mcangle_it1.018
r_mcbond_it0.718
r_angle_other_deg0.65
r_nbd_other0.192
r_nbd_refined0.182
r_mcbond_other0.178
r_symmetry_vdw_other0.174
r_nbtor_refined0.173
r_xyhbond_nbd_refined0.153
r_symmetry_hbond_refined0.144
r_symmetry_vdw_refined0.127
r_nbtor_other0.083
r_chiral_restr0.079
r_bond_refined_d0.008
r_gen_planes_refined0.005
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 Atoms1490
Nucleic Acid Atoms
Solvent Atoms104
Heterogen Atoms45

Software

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