5TO3

Crystal structure of thrombin mutant W215A/E217A fused to EGF456 of thrombomodulin via a 31-residue linker and bound to PPACK


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1DX5PDB ID 1DX5

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7293100 mM HEPES and 20% PEG 8000
Crystal Properties
Matthews coefficientSolvent content
360

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 62.939α = 90
b = 162.174β = 90
c = 128.859γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV++2014-08-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF1.5418

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
12.3444096.70.1060.10611.45.927169-0.2
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)
12.342.3991.50.4122.8

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ID 1DX52.3440-0.225770138896.40.2160.2140.255RANDOM47.7
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]
0.54-0.17-0.37
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.216
r_dihedral_angle_3_deg17.709
r_dihedral_angle_4_deg13.876
r_dihedral_angle_1_deg7.989
r_long_range_B_refined7.736
r_long_range_B_other7.608
r_scangle_other5.149
r_scbond_it3.563
r_scbond_other3.56
r_mcangle_it3.16
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.216
r_dihedral_angle_3_deg17.709
r_dihedral_angle_4_deg13.876
r_dihedral_angle_1_deg7.989
r_long_range_B_refined7.736
r_long_range_B_other7.608
r_scangle_other5.149
r_scbond_it3.563
r_scbond_other3.56
r_mcangle_it3.16
r_mcangle_other3.159
r_mcbond_it1.988
r_mcbond_other1.955
r_angle_refined_deg1.839
r_angle_other_deg0.991
r_chiral_restr0.092
r_bond_refined_d0.014
r_gen_planes_refined0.008
r_bond_other_d0.002
r_gen_planes_other0.002
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 Atoms3241
Nucleic Acid Atoms
Solvent Atoms93
Heterogen Atoms143

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling