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Crystal structure of thrombin in complex with inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other apo
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.3 298 The drop was made by mixing 1.5 ul of the thrombin-hirudin complex and 1.5 ul of reservior solution containing: Phosphate buffer pH7.3, 28% PEG, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.58 52.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.83 α = 90 b = 71.455 β = 100.35 c = 71.905 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MARRESEARCH 2007-09-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU300 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 1.8 70.71 100 0.07 0.065 7.7 7.1 32305 32305 1 1 26.5
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.8 1.85 100 0.57 0.53 1.4 6.9 2424
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 apo 1.8 70 29462 29462 1570 96.03 0.18393 0.18393 0.18222 0.1852 0.21456 0.2189 RANDOM 33.85
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] 0.77 -1.49 -1.05 -0.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.694 r_dihedral_angle_3_deg 12.888 r_dihedral_angle_4_deg 12.096 r_dihedral_angle_1_deg 5.859 r_scangle_it 3.467 r_scbond_it 2.138 r_mcangle_it 1.484 r_angle_refined_deg 1.301 r_mcbond_it 0.795 r_symmetry_vdw_refined 0.429
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.694 r_dihedral_angle_3_deg 12.888 r_dihedral_angle_4_deg 12.096 r_dihedral_angle_1_deg 5.859 r_scangle_it 3.467 r_scbond_it 2.138 r_mcangle_it 1.484 r_angle_refined_deg 1.301 r_mcbond_it 0.795 r_symmetry_vdw_refined 0.429 r_nbtor_refined 0.312 r_nbd_refined 0.2 r_symmetry_hbond_refined 0.178 r_xyhbond_nbd_refined 0.119 r_chiral_restr 0.089 r_metal_ion_refined 0.046 r_bond_refined_d 0.011 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2332 Nucleic Acid Atoms Solvent Atoms 277 Heterogen Atoms 29
Software Software Software Name Purpose REFMAC refinement MAR345dtb data collection MOSFLM data reduction SCALA data scaling CCP4 phasing