4Q1Y

Mutations Outside the Active Site of HIV-1 Protease Alter Enzyme Structure and Dynamic Ensemble of the Active Site to Confer Drug Resistance


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.2295126mM Phosphate buffer, 63mM Sodium Citrate, 24-29% Ammonium Sulfate, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties
Matthew coefficientSolvent content
2.141.56

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 50.813α = 90
b = 58.225β = 90
c = 61.824γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315Bent conical Si-mirror (Rh coated)2008-11-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 14-BM-C0.9002APS14-BM-C

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
11.539.2598.80.04816.86.5296332963333
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.51.5596.75

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT1.539.252977328079149798.720.18380.182530.20737RANDOM25.341
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]
-1.221.26-0.04
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.325
r_dihedral_angle_3_deg11.65
r_dihedral_angle_4_deg10.289
r_dihedral_angle_1_deg6.237
r_scangle_it2.464
r_scbond_it1.768
r_angle_refined_deg1.497
r_mcangle_it1.116
r_angle_other_deg0.876
r_mcbond_it0.817
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.325
r_dihedral_angle_3_deg11.65
r_dihedral_angle_4_deg10.289
r_dihedral_angle_1_deg6.237
r_scangle_it2.464
r_scbond_it1.768
r_angle_refined_deg1.497
r_mcangle_it1.116
r_angle_other_deg0.876
r_mcbond_it0.817
r_nbd_other0.204
r_nbd_refined0.199
r_mcbond_other0.199
r_symmetry_hbond_refined0.185
r_nbtor_refined0.171
r_xyhbond_nbd_refined0.144
r_symmetry_vdw_other0.131
r_chiral_restr0.1
r_symmetry_vdw_refined0.095
r_nbtor_other0.088
r_bond_refined_d0.009
r_gen_planes_refined0.005
r_gen_planes_other0.002
r_bond_other_d0.001
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_metal_ion_refined
r_xyhbond_nbd_other
r_mcangle_other
r_symmetry_hbond_other
r_scbond_other
r_metal_ion_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1506
Nucleic Acid Atoms
Solvent Atoms124
Heterogen Atoms65

Software

Software
Software NamePurpose
REFMACrefinement
ADSCdata collection
HKL-3000data reduction
HKL-3000data scaling
AMoREphasing