☰ Navigation Tabs
Crystal structure of E. faecium SHMT in complex with Me-THF and PLP-Gly
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7V3D
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 298 0.1M sodium cacodylate/hydrochloric acid pH 6.5, 2M ammonium sulfate, 0.2M sodium chloride
Crystal Properties Matthews coefficient Solvent content 3.81 67.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 126.981 α = 90 b = 126.981 β = 90 c = 170.106 γ = 90
Symmetry Space Group P 41 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 EIGER X 16M 2021-11-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 1 SPring-8 BL41XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.62 47.94 99.92 0.6592 0.1274 0.997 13.66 27 42482 54.56
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.62 2.714 3.464 0.6547 0.54 1.49
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 7V3D 2.62 47.94 1.35 42482 1999 99.83 0.1557 0.1538 0.1604 0.1943 0.1999 53.41
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 19.4819 f_angle_d 1.0067 f_chiral_restr 0.0576 f_bond_d 0.0079 f_plane_restr 0.0059
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6269 Nucleic Acid Atoms Solvent Atoms 197 Heterogen Atoms 139
Software Software Software Name Purpose BSS data collection XDS data reduction PHENIX phasing Coot model building PHENIX refinement