6DJ5

HIV-1 protease with mutation L76V in complex with GRL-0519 (tris-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 DROP5.22981.1 M NaCl, 0.1 M NaOAc, pH 5.2 4.1 mg/ml protease stock, 1:5 protease to inhibitor, 30% cryoprotectant
Crystal Properties
Matthews coefficientSolvent content
2.7254.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 58.672α = 90
b = 86.337β = 90
c = 45.997γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2015-04-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-BM1.0APS22-BM

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
11.75501000.06621.74.824343
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)
11.751.811000.4054.24.9

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-VALUE3NU31.7532242542430512111000.20080.20080.19840.2428RANDOM
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
271691
RMS Deviations
KeyRefinement Restraint Deviation
s_similar_adp_cmpnt0.064
s_non_zero_chiral_vol0.047
s_zero_chiral_vol0.036
s_from_restr_planes0.0269
s_angle_d0.023
s_anti_bump_dis_restr0.008
s_bond_d0.006
s_similar_dist
s_rigid_bond_adp_cmpnt
s_approx_iso_adps
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1510
Nucleic Acid Atoms
Solvent Atoms181
Heterogen Atoms42

Software

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