4Q1W

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
Matthews coefficientSolvent content
2.0840.94

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 50.741α = 90
b = 57.55β = 90
c = 61.809γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IVOSMIC Mirrors2008-09-18MSINGLE 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
11.8539.2298.590.06419.36.8158221582233
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.851.9295.25.31503

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Cut-off Sigma (I)Cut-off Sigma (F)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 REPLACEMENTTHROUGHOUT1.8539.2233160111499878798.590.174540.172880.20634RANDOM28.705
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]
-1.560.770.8
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.972
r_dihedral_angle_4_deg12.97
r_dihedral_angle_3_deg11.493
r_dihedral_angle_1_deg5.933
r_scangle_it2.004
r_angle_refined_deg1.342
r_scbond_it1.32
r_mcangle_it0.838
r_angle_other_deg0.835
r_mcbond_it0.582
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.972
r_dihedral_angle_4_deg12.97
r_dihedral_angle_3_deg11.493
r_dihedral_angle_1_deg5.933
r_scangle_it2.004
r_angle_refined_deg1.342
r_scbond_it1.32
r_mcangle_it0.838
r_angle_other_deg0.835
r_mcbond_it0.582
r_nbd_other0.198
r_nbd_refined0.186
r_symmetry_hbond_refined0.174
r_symmetry_vdw_other0.169
r_nbtor_refined0.168
r_symmetry_vdw_refined0.159
r_xyhbond_nbd_refined0.158
r_mcbond_other0.152
r_chiral_restr0.084
r_nbtor_other0.083
r_symmetry_hbond_other0.055
r_bond_refined_d0.008
r_gen_planes_refined0.004
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1490
Nucleic Acid Atoms
Solvent Atoms109
Heterogen Atoms62

Software

Software
Software NamePurpose
StructureStudiodata collection
AMoREphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling