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Crystal structure of P. abyssi tRNA m1A58 methyltransferase in complex with S-adenosyl-L-methionine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3LGA PDB code 3LGA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 291 2.8M ammonium sulfate, 0.2M ammonium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 3.65 66.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.55 α = 90 b = 89.26 β = 90 c = 110.32 γ = 90
Symmetry Space Group I 2 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 CCD ADSC QUANTUM 315r bi-morph mirrors 2010-02-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 0.98 SOLEIL PROXIMA 1
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 1.6 20 99.8 0.103 16.42 9.1 56562 22
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) 1.6 1.7 99.9 0.317 5.1 5.8 9295
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 code 3LGA 1.6 19.7 53652 2824 100 0.18473 0.18397 0.1818 0.19891 0.1981 RANDOM 25.151
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] 1.84 0.3 -2.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.229 r_dihedral_angle_3_deg 11.611 r_dihedral_angle_4_deg 11.294 r_dihedral_angle_1_deg 6.001 r_scangle_it 4.214 r_scbond_it 2.505 r_mcangle_it 1.538 r_angle_refined_deg 1.373 r_mcbond_it 0.823 r_chiral_restr 0.094
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.229 r_dihedral_angle_3_deg 11.611 r_dihedral_angle_4_deg 11.294 r_dihedral_angle_1_deg 6.001 r_scangle_it 4.214 r_scbond_it 2.505 r_mcangle_it 1.538 r_angle_refined_deg 1.373 r_mcbond_it 0.823 r_chiral_restr 0.094 r_bond_refined_d 0.012 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2054 Nucleic Acid Atoms Solvent Atoms 340 Heterogen Atoms 75
Software Software Software Name Purpose PHASER phasing REFMAC refinement XDS data reduction XSCALE data scaling