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Crystal structure of the methyltransferase PsiM in complex with s-adenosylmethionine (SAM)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8ZIE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 0.2 M Ammonium acetate, 0.1 M Sodium acetate trihydrate pH 4.6, 30% w/v Polyethylene glycol 4,000
Crystal Properties Matthews coefficient Solvent content 2.12 41.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.339 α = 90 b = 126.744 β = 90 c = 39.559 γ = 90
Symmetry Space Group P 21 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 PILATUS 6M 2023-05-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL18U1 0.97918 SSRF BL18U1
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 1.35 63.37 93.1 0.074 0.084 0.028 0.999 16.4 8.6 60331 12.65
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 1.35 1.43 64.2 0.593 0.694 0.307 0.672 2.7 4.7
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 8ZIE 1.35 31.7 1.35 60228 3036 93.08 0.1836 0.1825 0.1817 0.2038 0.2031 17
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 6.9065 f_angle_d 1.0201 f_chiral_restr 0.0759 f_plane_restr 0.0123 f_bond_d 0.0059
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2352 Nucleic Acid Atoms Solvent Atoms 200 Heterogen Atoms 27
Software Software Software Name Purpose PHENIX refinement autoPROC data reduction Aimless data scaling PHASER phasing