6E7J

HIV-1 wild type protease with GRL-042-17A, 3-phenylhexahydro-2h-cyclopenta[d]oxazol-2-one with a bicyclic oxazolidinone scaffold as the P2 ligand


X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 5.5
Temperature 298.0
Details 1.4M NACL, 0.1M SODIUM ACETATE PH 5.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 59.79 α = 90
b = 86.04 β = 90
c = 45.88 γ = 90
Symmetry
Space Group P 21 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD RAYONIX MX300HE -- 2017-10-25
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 22-ID 1.0 APS 22-ID

Data Collection

Overall
Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot
1.3 50 92.1 0.082 -- -- 6.7 -- 54309 -- -- --
High Resolution Shell
Resolution (High) Resolution (Low) Percent Possible (All) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All)
1.3 1.35 53.0 0.506 -- 2.1 2.4 --

Refinement

Statistics
Structure Solution Method Refinement High Resolution Refinement Low Resolution Cut-off Sigma (I) Cut-off Sigma (F) Number of Reflections (All) Number of Reflections (Observed) Number of Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work R-Free R-Free Selection Details
MOLECULAR REPLACEMENT 1.3 49.1 -- -- -- 51484 2772 92.01 -- 0.14971 0.14792 0.18234 RANDOM
High Resolution Shell
Refinement method Shell Resolution (High) Shell Resolution (Low) # of Reflections (Observed) # of Reflections (R-Free) # of Reflections (R-Work) R-Factor (R-Work) R-Factor (R-Free) R-Factor (R-Free Error) Percent Reflections (Observed)
X Ray Diffraction 1.3 1.334 -- 116 1972 0.251 0.257 -- 49.06
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 22.151
Anisotropic B[1][1] -1.62
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 1.13
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.5
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_2_deg 38.093
r_bond_other_d 0.002
r_rigid_bond_restr 5.609
r_mcbond_other 2.434
r_gen_planes_refined 0.012
r_angle_refined_deg 1.947
r_mcbond_it 2.469
r_angle_other_deg 1.036
r_scangle_other 4.986
r_long_range_B_refined 5.029
r_mcangle_other 2.954
r_dihedral_angle_1_deg 6.392
r_gen_planes_other 0.004
r_scbond_other 4.854
r_sphericity_bonded 21.7
r_dihedral_angle_3_deg 11.687
r_chiral_restr 0.136
r_bond_refined_d 0.018
r_sphericity_free 23.033
r_scbond_it 4.857
r_dihedral_angle_4_deg 17.827
r_long_range_B_other 5.029
r_mcangle_it 2.954
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1512
Nucleic Acid Atoms 0
Heterogen Atoms 52
Solvent Atoms 155

Software

Software
Software Name Purpose
REFMAC refinement version: 5.8.0222
HKL-2000 data scaling
PHASER phasing
SHELXL refinement version: 2014
HKL-2000 data reduction