6PRF

HIV-1 Protease multiple drug resistant clinical isolate mutant PR20 with GRL-14213A


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.52981.8 M sodium chloride, 0.1 M sodium acetate pH 5.5, 0.01M yittrium chloride
Crystal Properties
Matthew coefficientSolvent content
2.0540.03

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 60.565α = 90
b = 60.565β = 90
c = 85.139γ = 120
Symmetry
Space GroupP 61

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2018-10-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-ID1APS22-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)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
11.215099.70.0920.0980.0330.989217.54605921.518
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.211.25900.50.6230.3620.67622.3

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 DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE4YHQ1.2128.5543734219484.690.1540.15220.1897RANDOM21.518
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]
-0.03-0.02-0.030.11
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.518
r_dihedral_angle_4_deg18.84
r_rigid_bond_restr17.466
r_dihedral_angle_3_deg14.988
r_dihedral_angle_1_deg8.208
r_angle_refined_deg2.179
r_chiral_restr0.135
r_bond_refined_d0.015
r_gen_planes_refined0.015
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1518
Nucleic Acid Atoms
Solvent Atoms226
Heterogen Atoms105

Software

Software
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction