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Crystal structure of P. abyssi tRNA m1A58 methyltransferase in complex with S-adenosyl-L-homocysteine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3LHD PDB ENTRY 3LHD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 291 2.4M ammonium sulfate, 0.2M ammonium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 138.216 α = 90 b = 138.216 β = 90 c = 121.119 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 315r bi-morph mirrors 2009-06-26 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 2.05 34.86 99.8 0.091 11.5 4.8 162057 34.54
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) 2.05 2.16 100 0.706 2.1 4.8 23768
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 3LHD 2.05 34.86 153870 8116 99.76 0.19959 0.19862 0.21768 0.1835 RANDOM 38.427
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] 0.64 0.32 0.64 -0.96
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.819 r_dihedral_angle_4_deg 23.636 r_dihedral_angle_3_deg 17.294 r_dihedral_angle_1_deg 6.933 r_scangle_it 4.94 r_scbond_it 3.115 r_mcangle_it 1.995 r_angle_refined_deg 1.824 r_mcbond_it 1.248 r_nbtor_refined 0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.819 r_dihedral_angle_4_deg 23.636 r_dihedral_angle_3_deg 17.294 r_dihedral_angle_1_deg 6.933 r_scangle_it 4.94 r_scbond_it 3.115 r_mcangle_it 1.995 r_angle_refined_deg 1.824 r_mcbond_it 1.248 r_nbtor_refined 0.31 r_symmetry_vdw_refined 0.254 r_nbd_refined 0.21 r_chiral_restr 0.165 r_xyhbond_nbd_refined 0.138 r_symmetry_hbond_refined 0.102 r_bond_refined_d 0.019 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8152 Nucleic Acid Atoms Solvent Atoms 340 Heterogen Atoms 124
Software Software Software Name Purpose PHASER phasing REFMAC refinement XDS data reduction SCALA data scaling