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Crystal structure of human alpha-thrombin in complex with suramin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1PPB PDB ENTRY 1PPB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 291 100 mM tris, 25 % tert-butanol, 0.16 mM thrombin:suramin complex, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.78 55.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.966 α = 90 b = 76.202 β = 90 c = 113.848 γ = 90
Symmetry Space Group P 21 21 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 CCD MARRESEARCH 2005-10-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON LNLS BEAMLINE D03B-MX1 1.438 LNLS D03B-MX1
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 2.4 41.03 100 0.18 0.18 4.1 4.9 15625 27.82
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) 2.4 2.53 100 0.549 0.549 3.1 4.9 2233
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1PPB 2.4 41.03 3.1 14978 15579 781 99.98 0.184 0.184 0.18 0.266 0.2294 RANDOM 28.664
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] 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.293 r_dihedral_angle_3_deg 20.01 r_dihedral_angle_4_deg 19.907 r_dihedral_angle_1_deg 7.76 r_scangle_it 3.524 r_scbond_it 2.318 r_angle_refined_deg 2.059 r_mcangle_it 1.407 r_mcbond_it 0.812 r_nbtor_refined 0.326
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.293 r_dihedral_angle_3_deg 20.01 r_dihedral_angle_4_deg 19.907 r_dihedral_angle_1_deg 7.76 r_scangle_it 3.524 r_scbond_it 2.318 r_angle_refined_deg 2.059 r_mcangle_it 1.407 r_mcbond_it 0.812 r_nbtor_refined 0.326 r_nbd_refined 0.269 r_symmetry_hbond_refined 0.265 r_symmetry_vdw_refined 0.222 r_xyhbond_nbd_refined 0.174 r_chiral_restr 0.14 r_bond_refined_d 0.019 r_gen_planes_refined 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2282 Nucleic Acid Atoms Solvent Atoms 233 Heterogen Atoms 86
Software Software Software Name Purpose SCALA data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction