1T3R

HIV protease wild-type in complex with TMC114 inhibitor


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1F7A 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.23001 MG/ML PROTEIN; 5:1 LIGAND:PROTEIN; 30% AMSOR; SODIUM CITRATE AND SODIUM PHOSPHATE, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 300K
Crystal Properties
Matthews coefficientSolvent content
2.141.56

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 50.746α = 90
b = 57.807β = 90
c = 62.006γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray190CCDMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 5.0.10.900ALS5.0.1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
11.25095.50.0380.038255.55505655056
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.21.2476.20.3170.3174320

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 (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1F7A1.242.265500152226277595.520.140.13970.179RANDOM15.422
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]
-0.39-0.060.45
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free16.645
r_sphericity_bonded9.511
r_scangle_it8.132
r_dihedral_angle_1_deg6.96
r_scbond_it5.811
r_mcangle_it4.242
r_mcbond_it3.219
r_rigid_bond_restr2.59
r_angle_refined_deg1.593
r_angle_other_deg0.722
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free16.645
r_sphericity_bonded9.511
r_scangle_it8.132
r_dihedral_angle_1_deg6.96
r_scbond_it5.811
r_mcangle_it4.242
r_mcbond_it3.219
r_rigid_bond_restr2.59
r_angle_refined_deg1.593
r_angle_other_deg0.722
r_symmetry_hbond_refined0.338
r_symmetry_vdw_other0.312
r_symmetry_vdw_refined0.31
r_nbd_other0.274
r_xyhbond_nbd_refined0.254
r_nbd_refined0.244
r_chiral_restr0.149
r_nbtor_other0.095
r_bond_refined_d0.039
r_gen_planes_other0.028
r_gen_planes_refined0.021
r_bond_other_d0.007
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_mcbond_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1496
Nucleic Acid Atoms
Solvent Atoms259
Heterogen Atoms63

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMACrefinement