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PanDDA analysis group deposition -- Crystal Structure of FIBRINOGEN-LIKE GLOBE DOMAIN OF HUMAN TENASCIN-C in complex with Z2856434821
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 2.11 41.78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.1 α = 90 b = 77.1 β = 90 c = 71.6 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 2019-05-20 SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.91587 Diamond I04-1
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 1.67 71.6 100 0.094 0.099 0.028 1 16.7 12.5 25685
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 1.67 1.71 100 2.322 2.438 0.738 0.48 10.8 1864
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT 6QNV 1.67 54.52 24466 1165 99.94 0.1743 0.1724 0.2145 0.2049 RANDOM 27.968
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] 0.74 0.74 -1.49
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.355 r_dihedral_angle_4_deg 15.39 r_dihedral_angle_3_deg 12.827 r_dihedral_angle_1_deg 7.297 r_mcangle_it 3.67 r_mcbond_it 2.504 r_mcbond_other 2.502 r_angle_refined_deg 1.743 r_angle_other_deg 1.547 r_chiral_restr 0.092
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.355 r_dihedral_angle_4_deg 15.39 r_dihedral_angle_3_deg 12.827 r_dihedral_angle_1_deg 7.297 r_mcangle_it 3.67 r_mcbond_it 2.504 r_mcbond_other 2.502 r_angle_refined_deg 1.743 r_angle_other_deg 1.547 r_chiral_restr 0.092 r_bond_refined_d 0.011 r_gen_planes_refined 0.01 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1677 Nucleic Acid Atoms Solvent Atoms 174 Heterogen Atoms 13
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction REFMAC phasing