☰ Navigation Tabs
Crystal Structure of D-Dimer from Human Fibrin Complexed with Gly-His-Arg-Pro-Tyr-amide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1FZF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 295 equal volumes of (a) 9 mg/ml D-dimer, 2mM Gly-His-Arg-Pro-amide, 0.05M Tris, pH 7.0, 5mM CaCl2; (b) 10% PEG, 5mM CaCl2, 0.05M Tris, pH 8.0, 2mM sodium azide; The crystal was subsequently soaked in 0.5mM Gly-His-Arg-Pro-Tyr-amide in solution of came constitution., pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 295.0K
Crystal Properties Matthews coefficient Solvent content 2.76 55.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.63 α = 90 b = 148.69 β = 90 c = 232.68 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 ADSC QUANTUM 4 superbend 2006-01-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.1 1.0 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 2.66 50 99.9 0.071 14.4 9.7 56549 55743 1 1
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 2.66 2.76 99.6 0.294 7.9
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 (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 1FZF 2.7 30 1 53173 51522 96.9 0.22 0.2177 0.216 0.2204 0.275 0.2248 Random 40.916
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] 1.965 -11.105 9.14
RMS Deviations Key Refinement Restraint Deviation c_angle_deg 1.348 c_bond_d 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10581 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 65
Software Software Software Name Purpose CNS refinement PDB_EXTRACT data extraction ADSC data collection HKL-2000 data reduction HKL-2000 data scaling CNS phasing