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Crystal Structure of C412S Mutant of C0362 (TDE_0362 [TDE0362] resi 205-647)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9ARC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 7 296 0.1 M HEPES, pH 7.0, 0.1 M Sodium phosphate dibasic, 20% PEG 4,000
Crystal Properties Matthews coefficient Solvent content 2.22 44.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.402 α = 90 b = 99.327 β = 90 c = 120.006 γ = 90
Symmetry Space Group P 2 21 21
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 2021-11-22 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) 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 1.63 51.36 98.51 0.054 0.997 13.41 6.4 396707 24.67
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 1.63 1.65 82.2 0.569 0.826 1.43 4.5
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-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.63 51.36 1.34 118162 5983 98.51 0.1881 0.1868 0.1868 0.213 0.2134 37.56
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 14.492 f_angle_d 0.8316 f_chiral_restr 0.0559 f_plane_restr 0.0063 f_bond_d 0.0062
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3529 Nucleic Acid Atoms Solvent Atoms 320 Heterogen Atoms 39
Software Software Software Name Purpose DIALS data reduction xia2 data reduction Aimless data scaling pointless data scaling PHENIX phasing PHASER phasing Coot model building PHENIX refinement