☰ Navigation Tabs
Crystal structure of thrombin mutant W215A/E217A fused to EGF456 of thrombomodulin via a 31-residue linker and bound to PPACK
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1DX5 PDB ID 1DX5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 100 mM HEPES and 20% PEG 8000
Crystal Properties Matthews coefficient Solvent content 3 60
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.939 α = 90 b = 162.174 β = 90 c = 128.859 γ = 90
Symmetry Space Group C 2 2 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE RIGAKU RAXIS IV++ 2014-08-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5418
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) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.344 40 96.7 0.106 0.106 11.4 5.9 27169 -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) Redundancy Number Unique Reflections (All) 1 2.34 2.39 91.5 0.412 2.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ID 1DX5 2.34 40 -0.2 25770 1388 96.4 0.216 0.214 0.2199 0.255 0.2633 RANDOM 47.7
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 Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.216 r_dihedral_angle_3_deg 17.709 r_dihedral_angle_4_deg 13.876 r_dihedral_angle_1_deg 7.989 r_long_range_B_refined 7.736 r_long_range_B_other 7.608 r_scangle_other 5.149 r_scbond_it 3.563 r_scbond_other 3.56 r_mcangle_it 3.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.216 r_dihedral_angle_3_deg 17.709 r_dihedral_angle_4_deg 13.876 r_dihedral_angle_1_deg 7.989 r_long_range_B_refined 7.736 r_long_range_B_other 7.608 r_scangle_other 5.149 r_scbond_it 3.563 r_scbond_other 3.56 r_mcangle_it 3.16 r_mcangle_other 3.159 r_mcbond_it 1.988 r_mcbond_other 1.955 r_angle_refined_deg 1.839 r_angle_other_deg 0.991 r_chiral_restr 0.092 r_bond_refined_d 0.014 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.002 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 Atoms Number Protein Atoms 3241 Nucleic Acid Atoms Solvent Atoms 93 Heterogen Atoms 143
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling