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Crystal structure of the DRBD and CROPs of TcdA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4R04 4r04, 4NP4, 2G7C experimental model PDB 4NP4 4r04, 4NP4, 2G7C experimental model PDB 2G7C 4r04, 4NP4, 2G7C
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 291 0.1 M Bis-Tris pH 6.3, 0.6 M lithium sulfate
Crystal Properties Matthews coefficient Solvent content 4.54 72.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 379.507 α = 90 b = 187.641 β = 101.297 c = 95.324 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 PILATUS 6M-F 2019-08-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 0.9791 APS 24-ID-C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 3.18 186.1 99.07 0.283 0.944 4.43 3.5 108739 59.58
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.18 3.29 1.14 0.38
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 4r04, 4NP4, 2G7C 3.18 186.08 1.34 108739 5513 98.83 0.2091 0.2066 0.2082 0.2544 0.255 53.43
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 6.7387 f_angle_d 1.2122 f_chiral_restr 0.0731 f_bond_d 0.0106 f_plane_restr 0.0081
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 25441 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 180
Software Software Software Name Purpose XDS data scaling XDS data reduction PHENIX phasing PHENIX refinement