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S-Adenosylmethionine synthetase of Escherichia coli I103A in complex with (S,S)-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, SITTING DROP 8.56 293 23.3% EG, 9.5% PEG 8k, 0.029 M Lithium sulfate, 0.1 M Tris Base pH 8.56
Crystal Properties Matthews coefficient Solvent content 3.71 66.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 122.228 α = 90 b = 122.228 β = 90 c = 287.638 γ = 120
Symmetry Space Group P 61 2 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 2025-03-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, DESY BEAMLINE P11 1.033176 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 1.99 105.8 100 0.36 0.364 0.057 0.998 12.6 40.2 87996
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 1.99 2.09 100 4.794 4.855 0.765 0.513 40
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 2.09 99.34 1.33 75579 3907 99.98 0.1775 0.1764 0.1768 0.1986 0.1976
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 7.121 f_angle_d 0.775 f_chiral_restr 0.048 f_plane_restr 0.007 f_bond_d 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5813 Nucleic Acid Atoms Solvent Atoms 255 Heterogen Atoms 89
Software Software Software Name Purpose XDS data reduction autoPROC data processing Aimless data scaling PHASER phasing PHENIX refinement PDB_EXTRACT data extraction