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PanDDA analysis group deposition -- Crystal Structure of FIBRINOGEN-LIKE GLOBE DOMAIN OF HUMAN TENASCIN-C in complex with Z1251207602
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6QNV 6QNV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 MORPHEUS 0.09M NPS, 0.1M BUFFER SYSTEM 3 PH = 8.5, 50% V/V PRECIPITANT MIX 1
Crystal Properties Matthews coefficient Solvent content 2.14 42.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.46 α = 90 b = 77.46 β = 90 c = 71.72 γ = 90
Symmetry Space Group P 41 21 2
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 PILATUS 6M 2019-04-07 SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97625 Diamond I03
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 1.55 38.73 97.4 0.13 0.135 0.036 0.999 10.9 13.6 31322
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 1.55 1.59 94.7 3.014 3.125 0.821 0.504 14.2 2192
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 FOURIER SYNTHESIS THROUGHOUT 6QNV 1.55 38.76 29837 1461 97.01 0.181 0.1794 0.192 0.2146 0.2168 RANDOM 22.99
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] 0.72 0.72 -1.44
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.713 r_dihedral_angle_4_deg 17.103 r_dihedral_angle_3_deg 12.148 r_dihedral_angle_1_deg 6.901 r_mcangle_it 2.498 r_mcbond_it 1.884 r_mcbond_other 1.883 r_angle_refined_deg 1.83 r_angle_other_deg 1.555 r_chiral_restr 0.099
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.713 r_dihedral_angle_4_deg 17.103 r_dihedral_angle_3_deg 12.148 r_dihedral_angle_1_deg 6.901 r_mcangle_it 2.498 r_mcbond_it 1.884 r_mcbond_other 1.883 r_angle_refined_deg 1.83 r_angle_other_deg 1.555 r_chiral_restr 0.099 r_bond_refined_d 0.012 r_gen_planes_refined 0.011 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1683 Nucleic Acid Atoms Solvent Atoms 171 Heterogen Atoms 12
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction REFMAC phasing