6ZUH

Crystal Structure of Thrombin in complex with compound17


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP2830.02 M phosphate buffer pH 7.5, 27% PEG 8000, 100 mM NaCl
Crystal Properties
Matthews coefficientSolvent content
2.5251.16

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 70.091α = 90
b = 71.054β = 100.51
c = 72.62γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 300 mm plate2009-10-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-0071.541870

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym I (Observed)Rrim I (All)Rpim I (All)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
11.720.4382.60.0470.0470.0560.02917.93.43183931839
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Rrim I (All)Rpim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.71.7931.50.2650.0250.030.0161.9

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 REPLACEMENTTHROUGHOUTinhouse1.71530248158982.510.18020.17810.2178RANDOM26.847
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]
0.21-0.27-0.550.41
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.328
r_dihedral_angle_3_deg13.406
r_dihedral_angle_4_deg12.234
r_dihedral_angle_1_deg6.793
r_angle_refined_deg2.342
r_chiral_restr0.106
r_bond_refined_d0.012
r_gen_planes_refined0.012
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2348
Nucleic Acid Atoms
Solvent Atoms311
Heterogen Atoms48

Software

Software
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction