2CF9

Complex of recombinant human thrombin with an inhibitor


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1OYTPDB ENTRY 1OYT

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.4PH 7.40
Crystal Properties
Matthews coefficientSolvent content
2.7643

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 71.29α = 90
b = 71.84β = 100.56
c = 73.06γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCHOSMIC MIRRORS2004-10-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODEENRAF-NONIUS FR591

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
11.792091.40.0422.94.5431281-3
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)
11.791.986.60.255.44.13

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 SYNTHESISTHROUGHOUTPDB ENTRY 1OYT1.7971.829702158291.50.1620.160.198RANDOM21.94
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]
-0.8-0.440.14
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.102
r_dihedral_angle_4_deg12.718
r_dihedral_angle_3_deg11.608
r_dihedral_angle_1_deg6.117
r_scangle_it2.498
r_scbond_it1.607
r_angle_refined_deg1.359
r_mcangle_it1.035
r_mcbond_it0.59
r_nbtor_refined0.307
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.102
r_dihedral_angle_4_deg12.718
r_dihedral_angle_3_deg11.608
r_dihedral_angle_1_deg6.117
r_scangle_it2.498
r_scbond_it1.607
r_angle_refined_deg1.359
r_mcangle_it1.035
r_mcbond_it0.59
r_nbtor_refined0.307
r_nbd_refined0.19
r_symmetry_hbond_refined0.175
r_symmetry_vdw_refined0.15
r_xyhbond_nbd_refined0.135
r_chiral_restr0.09
r_bond_refined_d0.012
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_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2301
Nucleic Acid Atoms
Solvent Atoms494
Heterogen Atoms35

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling