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Crystal Structure of D-Dimer from Human Fibrin Complexed with Met-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, 2 mM Gly-His-Arg-Pro-amide, 0.05 M Tris, pH 7.0,
5 mM CaCl2 and (b) 10% PEG, 5 mM CaCl2, 0.05M Tris, pH 8.0, 2 mM sodium azide.
Crystals were subsequently soaked in same solution containing 0.6 mM Met-His-Arg-Pro-Tyr-amide., pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 295.0K
Crystal Properties Matthews coefficient Solvent content 2.7 54.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.38 α = 90 b = 147.23 β = 90 c = 231.48 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 IMAGE PLATE MAR scanner 345 mm plate Confocal Max-Flux Optic 2006-11-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.54
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 2.8 50 95.4 0.085 3.5 46081 44180
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 2.8 2.9 83.5 0.572 2.5
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 1FZF 2.8 30 1 46081 43088 92 0.2164 0.2159 0.2202 0.276 0.2223 Random 40.6025
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] 0.528 11.776 -12.304
RMS Deviations Key Refinement Restraint Deviation c_mcangle_it 1.185 c_scangle_it 0.805 c_mcbond_it 0.634 c_scbond_it 0.425 c_bond_d c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot
RMS Deviations Key Refinement Restraint Deviation c_mcangle_it 1.185 c_scangle_it 0.805 c_mcbond_it 0.634 c_scbond_it 0.425 c_bond_d c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d c_improper_angle_d_na c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10587 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 64
Software Software Software Name Purpose CNS refinement PDB_EXTRACT data extraction MAR345dtb data collection DENZO data reduction SCALEPACK data scaling CNS phasing