2QI7

Crystal structure of protease inhibitor, MIT-2-AD86 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
2.141.51

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 50.798α = 90
b = 58.037β = 90
c = 61.758γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray200IMAGE PLATERIGAKU RAXIS Vosmic mirrors2006-01-01MSINGLE 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
11.855099.90.0585.812.75.516171

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 (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTpdb entry 1F7A1.8542.3153181531881099.850.175170.175170.173640.20339RANDOM18.626
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]
-0.1-0.080.18
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.314
r_dihedral_angle_4_deg23.082
r_dihedral_angle_3_deg11.28
r_dihedral_angle_1_deg6.007
r_scangle_it1.66
r_angle_refined_deg1.215
r_scbond_it1.09
r_mcangle_it0.726
r_angle_other_deg0.685
r_mcbond_it0.526
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.314
r_dihedral_angle_4_deg23.082
r_dihedral_angle_3_deg11.28
r_dihedral_angle_1_deg6.007
r_scangle_it1.66
r_angle_refined_deg1.215
r_scbond_it1.09
r_mcangle_it0.726
r_angle_other_deg0.685
r_mcbond_it0.526
r_nbd_refined0.181
r_nbd_other0.18
r_symmetry_vdw_other0.173
r_nbtor_refined0.165
r_xyhbond_nbd_refined0.128
r_symmetry_hbond_refined0.127
r_mcbond_other0.112
r_symmetry_vdw_refined0.096
r_nbtor_other0.081
r_chiral_restr0.072
r_bond_refined_d0.008
r_gen_planes_refined0.003
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 Atoms143
Heterogen Atoms59

Software

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