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Structure of plasmin and peptide complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6D3X
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5 293 100 mM Sodium Citrate,
100 mM MgCl2,
18% PEG 4000
Crystal Properties Matthews coefficient Solvent content 2.33 47.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.228 α = 90 b = 80.293 β = 90 c = 83.198 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 315r 2018-12-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.953732013702 Australian Synchrotron MX2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 2.3467 46.6908 98.87 0.189 0.214 0.097 0.991 5 4.2 22667 21.72
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.347 2.431 98.03 0.714 0.814 0.379 0.819 1.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 6d3x 2.3467 46.6908 1.33 22557 993 98.85 0.2352 0.2328 0.2328 0.2874 0.2892 26.37
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 16.5829 f_angle_d 0.7023 f_chiral_restr 0.0509 f_plane_restr 0.0053 f_bond_d 0.0041
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3915 Nucleic Acid Atoms Solvent Atoms 172 Heterogen Atoms 6
Software Software Software Name Purpose PHENIX refinement XDS data reduction SCALA data scaling PHASER phasing