3EM4

Crystal structure of atazanavir (ATV) in complex with I50L/A71V drug-resistant HIV-1 protease


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.2300pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 300K
Crystal Properties
Matthew coefficientSolvent content
2.0941.1

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 51.231α = 90
b = 59.54β = 82.22
c = 59.863γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray200IMAGE PLATERIGAKU RAXIS IVYale Mirrors2007-08-17MSINGLE 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)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
12.15095.80.06914.00735670120006
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.12.1890.10.4931867

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 DIFFRACTIONTHROUGHOUT1F7A2.14020000101695.790.1830.1790.249RANDOM38.666
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]
-2.130.251.041.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.71
r_dihedral_angle_4_deg20.246
r_dihedral_angle_3_deg15.567
r_dihedral_angle_1_deg7.243
r_scangle_it2.274
r_scbond_it1.585
r_angle_refined_deg1.413
r_mcangle_it1.068
r_mcbond_it0.888
r_angle_other_deg0.719
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.71
r_dihedral_angle_4_deg20.246
r_dihedral_angle_3_deg15.567
r_dihedral_angle_1_deg7.243
r_scangle_it2.274
r_scbond_it1.585
r_angle_refined_deg1.413
r_mcangle_it1.068
r_mcbond_it0.888
r_angle_other_deg0.719
r_symmetry_vdw_other0.248
r_symmetry_hbond_refined0.215
r_nbd_other0.202
r_symmetry_vdw_refined0.198
r_nbd_refined0.189
r_xyhbond_nbd_refined0.182
r_nbtor_refined0.174
r_mcbond_other0.164
r_nbtor_other0.087
r_chiral_restr0.08
r_bond_refined_d0.008
r_gen_planes_refined0.006
r_bond_other_d0.002
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2937
Nucleic Acid Atoms
Solvent Atoms156
Heterogen Atoms137

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
AMoREphasing