6TFI

PXR IN COMPLEX WITH THROMBIN INHIBITOR COMPOUND 17


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3HVL 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP82771 MICROLITER PROTEIN AT 12.1 MG/ML (IN 20 MILLIMOLAR TRIS PH 7.8, 250 MILLIMOLAR NACL, 2.5 MILLIMOLAR EDTA, 5% (V/V) GLYCEROL, 5 MM DTT), PREINCUBATED WITH 25 MILLIMOLAR COMPOUND 17 (FROM 500 MILLIMOLAR STOCK IN DMSO) for 24 hours at 277 K, MIXED WITH 1 MICROLITER OF RESERVOIR (100 MILLIMOLAR IMIDAZOLE PH 8.0, 20 % (V/V) MPD). CRYO BUFFER 100 MILLIMOLAR IMIDAZOLE PH 8.0, 30 % (V/V) MPD
Crystal Properties
Matthews coefficientSolvent content
2.5651.94

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 85.356α = 90
b = 88.964β = 90
c = 105.658γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2010-10-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.10.91841BESSY14.1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)Rrim I (All)CC (Half)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
11.8544.4897.90.0530.0590.99917.155.076792539.61
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Rrim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.851.9698.70.8780.9770.6681.825

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 DIFFRACTIONFOURIER SYNTHESISTHROUGHOUT3HVL1.8544.4865823210197.90.172760.171920.19932RANDOM41.918
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]
-0.60.250.35
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.873
r_dihedral_angle_3_deg14.978
r_dihedral_angle_4_deg14.137
r_long_range_B_refined9.443
r_long_range_B_other9.404
r_scangle_other6.625
r_dihedral_angle_1_deg5.192
r_mcangle_it4.67
r_mcangle_other4.669
r_scbond_it4.209
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.873
r_dihedral_angle_3_deg14.978
r_dihedral_angle_4_deg14.137
r_long_range_B_refined9.443
r_long_range_B_other9.404
r_scangle_other6.625
r_dihedral_angle_1_deg5.192
r_mcangle_it4.67
r_mcangle_other4.669
r_scbond_it4.209
r_scbond_other4.208
r_mcbond_it3.081
r_mcbond_other3.081
r_angle_refined_deg1.308
r_angle_other_deg1.265
r_chiral_restr0.074
r_bond_refined_d0.005
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4847
Nucleic Acid Atoms
Solvent Atoms360
Heterogen Atoms89

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing