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Crystal structure of the complex between thrombin and the central "E" region of fibrin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1PPB PDB entries 1PPB, 1JY2 experimental model PDB 1JY2 PDB entries 1PPB, 1JY2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICRODIALYSIS 7.9 298 PEG 3500, AMMONIUM PHOSPHATE, TRIS, pH 7.90, MICRODIALYSIS, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.89 55.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.263 α = 90 b = 76.263 β = 90 c = 192.452 γ = 120
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 MARRESEARCH COLLIMATOR M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE SIEMENS
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 3.65 31.24 96.3 3.4 26890
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.65 3.78 87.6 1.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 entries 1PPB, 1JY2 3.65 19.7 25847 2390 93.4 0.221 0.2137 0.29 0.2835 RANDOM
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]
RMS Deviations Key Refinement Restraint Deviation s_bond_d 0.013 s_angle_d s_similar_dist s_from_restr_planes s_zero_chiral_vol s_non_zero_chiral_vol s_anti_bump_dis_restr s_rigid_bond_adp_cmpnt s_similar_adp_cmpnt s_approx_iso_adps
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6834 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 70
Software Software Software Name Purpose d*TREK data scaling d*TREK data reduction CNS refinement SHELXL-97 refinement CNS phasing