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Crystal structure of the catalytic domain of MmOmeRS, an O-methyl tyrosyl-tRNA synthetase evolved from Methanosarcina mazei PylRS, complexed with O-methyl tyrosine and AMP-PNP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2ZCE PDB ENTRY 2ZCE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 298 11% PEG MME 2000, 100mM TRIS-HCl pH7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 3.39 63.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 104.809 α = 90 b = 104.809 β = 90 c = 71.674 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 2010-10-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.2 1.0 ALS 8.2.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 50 99.7 0.037 35.06 10.2 45085 44965 -3 35.266
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.75 1.86 98.9 0.382 4.26 6.4 7238
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2ZCE 1.75 42.3 45085 44961 2268 99.78 0.1849 0.1834 0.1829 0.2124 0.2096 RANDOM 29.9312
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 r_dihedral_angle_2_deg 32.947 r_dihedral_angle_4_deg 17.189 r_dihedral_angle_3_deg 14.381 r_dihedral_angle_1_deg 5.793 r_scangle_it 3.583 r_scbond_it 2.083 r_mcangle_it 1.488 r_angle_refined_deg 1.305 r_mcbond_it 0.774 r_chiral_restr 0.086
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.947 r_dihedral_angle_4_deg 17.189 r_dihedral_angle_3_deg 14.381 r_dihedral_angle_1_deg 5.793 r_scangle_it 3.583 r_scbond_it 2.083 r_mcangle_it 1.488 r_angle_refined_deg 1.305 r_mcbond_it 0.774 r_chiral_restr 0.086 r_bond_refined_d 0.01 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2102 Nucleic Acid Atoms Solvent Atoms 235 Heterogen Atoms 67
Software Software Software Name Purpose XSCALE data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction XDS data scaling XDS data reduction