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Structure of a Covalently Captured Collagen Triple Helix using Lysine-Glutamate Pairs
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3T4F
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 293 3.5 M sodium formate, 0.1 M BIS-TRIS, pH 7.0
Crystal Properties Matthews coefficient Solvent content 1.74 29.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 134.835 α = 90 b = 14.113 β = 90.35 c = 24.568 γ = 90
Symmetry Space Group C 1 2 1
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 X 16M Adjustable focus K-B pair 2019-10-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-B 1.033 APS 23-ID-B
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 1.37 33.71 93.5 0.149 0.157 0.046 0.998 8.7 11.2 9559
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 1.37 1.41 59.5 1.014 1.096 0.406 0.727 6.9
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 THROUGHOUT 3t4f 1.37 33.71 1.36 9539 463 93.37 0.1582 0.1571 0.1573 0.1774 0.1772 14.0822
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 11.557 f_angle_d 1.661 f_chiral_restr 0.052 f_bond_d 0.013 f_plane_restr 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 474 Nucleic Acid Atoms Solvent Atoms 145 Heterogen Atoms
Software Software Software Name Purpose xia2 data reduction DIALS data reduction Aimless data scaling PHASER phasing PHENIX refinement PDB_EXTRACT data extraction