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Crystal structure of Tm1570 domain from Calditerrivibrio nitroreducens in complex with S-adenosyl-L-methionine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8B1N
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293.15 Protein solution: 20 mg/mL Tm1570 in 50 mM HEPES buffer pH 7.4, 300 mM NaCl, 5% glycerol, with addition of 5 mM SAM, 5 mM MgCl2, 0.1% DDM. Reservoir solution: 0.1 M Tris pH 8.5, 20% v/v ethanol.
Crystal Properties Matthews coefficient Solvent content 1.94 36.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 105.85 α = 90 b = 48.09 β = 116.22 c = 79.81 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 PILATUS3 6M 2022-09-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.9184 BESSY 14.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim 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 1.95 47.48 98.4 0.073 0.997 10.04 3.31 26147 36.82
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.95 2.07 99.4 0.959 0.696 1.3 3.44
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 1.95 30.66 1.34 26122 1999 98.49 0.2093 0.206 0.2073 0.25 0.2499 51.99
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 17.927 f_angle_d 0.9453 f_chiral_restr 0.0599 f_bond_d 0.0068 f_plane_restr 0.0055
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2545 Nucleic Acid Atoms Solvent Atoms 103 Heterogen Atoms 54
Software Software Software Name Purpose MxCuBE data collection XDS data reduction XDS data scaling PHASER phasing PHENIX refinement Coot model building