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Crystal structure of TrmD 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 Protein sample: 4 mg/mL TrmD in 50 mM HEPES buffer pH 7.4, 300 mM NaCl, 5% glycerol, 10 mM SAM, 20 mM MgCl2. Reservoir solution: 0.2 M sodium thiocyanate, 20% w/v PEG 3350 (JCSG+ screen 1-14).
Crystal Properties Matthews coefficient Solvent content 3.51 65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.39 α = 90 b = 85.39 β = 90 c = 210.71 γ = 90
Symmetry Space Group P 43 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 EIGER2 X CdTe 16M 2022-10-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2) 0.465220 PETRA III, EMBL c/o DESY P14 (MX2)
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 2.19 45.79 99.1 0.133 0.998 11.93 8.75 40840 32.88
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 2.19 2.32 95.1 1.018 0.72 1.8 5.67
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 8B1N 2.19 44.83 1.34 40820 2040 99.08 0.1687 0.1665 0.1677 0.2088 0.209 40.66
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 17.2482 f_angle_d 0.8573 f_chiral_restr 0.0525 f_bond_d 0.007 f_plane_restr 0.0049
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3836 Nucleic Acid Atoms Solvent Atoms 396 Heterogen Atoms 83
Software Software Software Name Purpose MxCuBE data collection XDS data reduction XDS data scaling PHASER phasing Coot model building PHENIX refinement