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2.2 Angstrom crystal structure of the complex between Bovine Thrombin and Sucrose Octasulfate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1MKX PDB ENTRY 1MKX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.2 295 3 microliters Bovine thrombin, 7 mg/ml in 0.01M Tris-HCl, ph 8.0, 0.05M NaCl, 0.1M sodium citrate, 20% w/v, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.77 55.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.562 α = 90 b = 87.562 β = 90 c = 191.99 γ = 90
Symmetry Space Group P 43 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 104 IMAGE PLATE RIGAKU RAXIS IV++ Rigaku Varimax Confocal optics 2004-06-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.2 27.92 99.8 0.083 13.4 7.87 38833 38745
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 2.2 2.28 100 0.311 6.3 9.03 3775
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 (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 ENTRY 1MKX 2.2 27.8 38784 36728 1938 99.78 0.20574 0.20373 0.2185 0.24456 0.2552 RANDOM 45.187
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] -0.15 -0.15 0.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.213 r_dihedral_angle_4_deg 17.337 r_dihedral_angle_3_deg 15.513 r_dihedral_angle_1_deg 5.498 r_scangle_it 3.491 r_scbond_it 2.342 r_mcangle_it 1.344 r_angle_refined_deg 1.244 r_mcbond_it 0.622 r_chiral_restr 0.079
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.213 r_dihedral_angle_4_deg 17.337 r_dihedral_angle_3_deg 15.513 r_dihedral_angle_1_deg 5.498 r_scangle_it 3.491 r_scbond_it 2.342 r_mcangle_it 1.344 r_angle_refined_deg 1.244 r_mcbond_it 0.622 r_chiral_restr 0.079 r_bond_refined_d 0.008 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4393 Nucleic Acid Atoms Solvent Atoms 253 Heterogen Atoms 138
Software Software Software Name Purpose CrystalClear data collection PHASER phasing REFMAC refinement d*TREK data reduction d*TREK data scaling