2P3D

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


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelOtherCrystal Structure of the multi-drug resistant mutant subtype B HIV protease complexed with TL-3 inhibitor

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.22910.64M ammonium sulfate, 0.1M sodium cacodylate. The crystals nucleated at 277K and were transfered to 291K for further growth, pH 6.2, VAPOR DIFFUSION, HANGING DROP
Crystal Properties
Matthews coefficientSolvent content
2.0539.96

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 61.253α = 90
b = 61.253β = 90
c = 82.231γ = 120
Symmetry
Space GroupP 61

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mm2004-09-01MSINGLE 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
12.154.7299.70.07513.63.74354
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)
12.12.211000.4142.73.7

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTCrystal Structure of the multi-drug resistant mutant subtype B HIV protease complexed with TL-3 inhibitor2.830.63392741999.930.189960.182930.25989RANDOM44.41
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]
-0.04-0.02-0.040.06
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.771
r_dihedral_angle_4_deg20.505
r_dihedral_angle_3_deg16.225
r_sphericity_bonded10.462
r_dihedral_angle_1_deg6.271
r_scangle_it4.378
r_mcangle_it3.141
r_scbond_it2.958
r_rigid_bond_restr2.035
r_mcbond_it1.751
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.771
r_dihedral_angle_4_deg20.505
r_dihedral_angle_3_deg16.225
r_sphericity_bonded10.462
r_dihedral_angle_1_deg6.271
r_scangle_it4.378
r_mcangle_it3.141
r_scbond_it2.958
r_rigid_bond_restr2.035
r_mcbond_it1.751
r_angle_refined_deg1.69
r_nbtor_refined0.337
r_symmetry_hbond_refined0.325
r_nbd_refined0.256
r_symmetry_vdw_refined0.238
r_xyhbond_nbd_refined0.148
r_chiral_restr0.096
r_bond_refined_d0.015
r_gen_planes_refined0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_sphericity_free
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1526
Nucleic Acid Atoms
Solvent Atoms50
Heterogen Atoms66

Software

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