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S-Adenosylmethionine synthetase of Thermococcus kodakarensis in complex with (S,R)-SAM and PPNP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1RG9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 293 25% EG, 10% PEG 8k, 0.04 M Li Acetate, 0.1 M Tris Base pH 8.5
Crystal Properties Matthews coefficient Solvent content 2.43 49.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 134.767 α = 90 b = 58.995 β = 104.32 c = 236.259 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 EIGER X 16M 2024-04-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, DESY BEAMLINE P11 1.03321 PETRA III, DESY P11
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.11 114.46 99 0.143 0.155 0.058 0.994 7.6 7 103091
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.11 2.22 98.8 0.68 0.736 0.278 0.956 6.9
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 THROUGHOUT 2.11 67.33 1.35 102796 5229 98.51 0.1961 0.194 0.1956 0.2364 0.2346
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 4.629 f_angle_d 0.576 f_chiral_restr 0.047 f_plane_restr 0.003 f_bond_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12505 Nucleic Acid Atoms Solvent Atoms 563 Heterogen Atoms 135
Software Software Software Name Purpose PHENIX refinement autoPROC data processing Aimless data scaling XDS data reduction PHASER phasing PDB_EXTRACT data extraction