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Structure of Saccharomyces cerevisiae mRNA cap (guanine-N7) methyltransferase, Abd1, in complex with SAH
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9MG0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.5 292 0.8 M Sodium Phosphate, 1.2 M Potassium Phosphate, and 0.1 M Sodium Acetate
Crystal Properties Matthews coefficient Solvent content 3.16 61.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 95.16 α = 90 b = 95.16 β = 90 c = 248.942 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 315 2015-10-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A 0.98 NSLS X29A
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 1.75 24.83 100 0.186 0.194 0.057 0.989 9 11.3 43915
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 1.75 1.79 100 0.606 0.637 0.196 0.897 10.4
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 FREE R-VALUE 1.75 24.83 1.35 43909 2279 99.98 0.1648 0.1637 0.164 0.1863 0.1867
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 18.278 f_angle_d 0.811 f_chiral_restr 0.054 f_plane_restr 0.007 f_bond_d 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2411 Nucleic Acid Atoms Solvent Atoms 313 Heterogen Atoms 42
Software Software Software Name Purpose PHENIX refinement Aimless data scaling iMOSFLM data reduction PHASER phasing