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Crystal structure of sulfo-hirudin complexed to thrombin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4HTC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 298 0.1M Tris, 20% PEG2K, 0.01M Nickel Chloride. , pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.44 49.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.074 α = 90 b = 103.567 β = 90 c = 139.184 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 CCD ADSC QUANTUM 4 2007-04-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.1 1.00 ALS 5.0.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.84 47.95 95.75 0.099 282 4.6 34309 32851 5
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.84 1.91 94.6 0.645 10.5 3.5 3165
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 4HTC 1.84 47.95 2 34309 32851 1649 95.75 0.177 0.175 0.1944 0.233 0.2385 RANDOM 34.397
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] 0.03 -0.43 0.4
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.292 r_dihedral_angle_4_deg 17.902 r_dihedral_angle_3_deg 17.347 r_dihedral_angle_1_deg 6.194 r_scangle_it 5.146 r_scbond_it 3.857 r_mcangle_it 2.443 r_angle_refined_deg 1.643 r_mcbond_it 1.615 r_nbtor_refined 0.316
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.292 r_dihedral_angle_4_deg 17.902 r_dihedral_angle_3_deg 17.347 r_dihedral_angle_1_deg 6.194 r_scangle_it 5.146 r_scbond_it 3.857 r_mcangle_it 2.443 r_angle_refined_deg 1.643 r_mcbond_it 1.615 r_nbtor_refined 0.316 r_xyhbond_nbd_refined 0.237 r_nbd_refined 0.219 r_symmetry_vdw_refined 0.187 r_chiral_restr 0.151 r_symmetry_hbond_refined 0.133 r_metal_ion_refined 0.023 r_bond_refined_d 0.016 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2779 Nucleic Acid Atoms Solvent Atoms 221 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction ADSC data collection HKL-2000 data reduction SCALEPACK data scaling AMoRE phasing