2P3A

Crystal Structure of the multi-drug resistant mutant subtype B HIV protease complexed with TL-3 inhibitor


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelOtherThe same structure previously solved in space group P6(1)22

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.22916% (v/v) MPD, 0.32M ammonium sulfate, 0.1M sodium cacodylate, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
2.0339.54

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 60.931α = 90
b = 60.931β = 90
c = 82.463γ = 120
Symmetry
Space GroupP 61

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mm2004-01-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONLNLS BEAMLINE D03B-MX1LNLSD03B-MX1

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
11.7552.7899.60.03717.84.8174921749226.415
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)
11.751.841000.3483.44.82569

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)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 REPLACEMENTTHROUGHOUTThe same structure previously solved in space group P6(1)221.7519.21746788499.630.1850.1850.1830.232RANDOM30.161
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]
-0.02-0.01-0.020.03
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.348
r_dihedral_angle_4_deg19.147
r_dihedral_angle_3_deg13.121
r_sphericity_bonded11.754
r_dihedral_angle_1_deg6.353
r_scangle_it3.709
r_scbond_it2.701
r_mcangle_it2.639
r_rigid_bond_restr1.829
r_angle_refined_deg1.777
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.348
r_dihedral_angle_4_deg19.147
r_dihedral_angle_3_deg13.121
r_sphericity_bonded11.754
r_dihedral_angle_1_deg6.353
r_scangle_it3.709
r_scbond_it2.701
r_mcangle_it2.639
r_rigid_bond_restr1.829
r_angle_refined_deg1.777
r_mcbond_it1.647
r_nbtor_refined0.33
r_symmetry_hbond_refined0.289
r_nbd_refined0.255
r_xyhbond_nbd_refined0.191
r_symmetry_vdw_refined0.189
r_chiral_restr0.095
r_bond_refined_d0.015
r_gen_planes_refined0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1518
Nucleic Acid Atoms
Solvent Atoms186
Heterogen Atoms66

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
MAR345data collection
MOSFLMdata reduction
CCP4data scaling
PHASERphasing