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Crystal Structure of Human PTX3 C-terminal domain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3KQR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 10% w/v PEG 8000, 20% v/v ethylene glycol, 0.03 M of each halide, 0.1 M MOPS/HEPES-Na pH 7.5) * 0.3 M sodium fluoride, 0.3 M sodium bromide, 0.3 M sodium iodide
Crystal Properties Matthews coefficient Solvent content 2.82 56.36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 138.003 α = 90 b = 138.003 β = 90 c = 69.55 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS EIGER R 4M 2019-05-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.9159 Diamond I04-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.43 45.33 99.54 0.044 0.998 8.66 6.5 9663 62.77
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.43 2.517 99.37 0.66 0.892 1.08
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.43 45.33 1.34 9637 483 99.49 0.2187 0.2164 0.2623 0.234 69.94
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 5.516 f_angle_d 0.7898 f_chiral_restr 0.0546 f_bond_d 0.0088 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1546 Nucleic Acid Atoms Solvent Atoms 21 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement xia2 data reduction DIALS data scaling PHASER phasing