6DJ7

HIV-1 protease with mutation L76V in complex with GRL-5010 (gem-difluoro-bis-tetrahydrofuran as P2 ligand)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3NU3 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.22981.15 M NaCl, 0.1 M NaOAc, pH 5.2 4.1 mg/ml protease stock, 1:5 protease to inhibitor 1:1 liquor to sample, soaked in 30% glycerol cryoprotectant
Crystal Properties
Matthews coefficientSolvent content
2.754.48

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 58.264α = 90
b = 86.053β = 90
c = 46.252γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX300-HS2016-02-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-ID1.0APS22-ID

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
11.3150960.08713.34.455212
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)
11.311.3677.60.4542.11.8

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE3NU31.313254659552122663960.16090.16090.15830.2049RANDOM
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]
Coordinate Error
Structure Solution MethodRefinement High ResolutionRefinement Low Resolution
991703.4
RMS Deviations
KeyRefinement Restraint Deviation
s_non_zero_chiral_vol0.08
s_approx_iso_adps0.077
s_zero_chiral_vol0.068
s_similar_adp_cmpnt0.048
s_angle_d0.032
s_from_restr_planes0.0296
s_anti_bump_dis_restr0.027
s_bond_d0.012
s_rigid_bond_adp_cmpnt0.004
s_similar_dist
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1510
Nucleic Acid Atoms
Solvent Atoms217
Heterogen Atoms40

Software

Software
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
SHELXL-97refinement