3H5B

Crystal structure of wild type HIV-1 protease with novel P1'-ligand GRL-02031


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3DJKPDB entry 3DJK

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5298Inhibitor GRL-02031 was dissolved in dimethylsulfoxide (DMSO). Crystals were grown using 1:5 molar ratio of protease (at 3.9 mg/ml) to inhibitor. The reservoir contained 0.1 M citrate phosphate buffer, pH 5.0, 0.35 M NaCl and 4% DMSO. Crystals were mounted on a nylon loop and flash-frozen in liquid nitrogen with a cryoprotectant of 30% v/v glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.6954.22

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 58.111α = 90
b = 86.416β = 90
c = 45.97γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 300 mm plate2008-06-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-ID0.8000APS22-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
11.295092.50.055276.6546285462813.5
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)
11.291.3464.30.4912.273.93723

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 RPDB entry 3DJK1.29105442854428272692.50.14360.14360.14160.1813RANDOM
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
1816381720.05
RMS Deviations
KeyRefinement Restraint Deviation
s_approx_iso_adps0.087
s_non_zero_chiral_vol0.071
s_zero_chiral_vol0.062
s_similar_adp_cmpnt0.054
s_angle_d0.031
s_from_restr_planes0.028
s_anti_bump_dis_restr0.024
s_bond_d0.012
s_rigid_bond_adp_cmpnt0.004
s_similar_dist
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1512
Nucleic Acid Atoms
Solvent Atoms205
Heterogen Atoms51

Software

Software
Software NamePurpose
MAR345data collection
AMoREphasing
SHELXL-97refinement
HKL-2000data reduction
HKL-2000data scaling