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Crystal structure of tRNA (Um34/Cm34) methyltransferase TrmL from Escherichia coli with SAH
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4JAK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 289 25% PEG 4000, 5% glycerol, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 1.91 35.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.276 α = 90 b = 66.291 β = 99.24 c = 49.768 γ = 90
Symmetry Space Group P 1 21 1
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 2011-03-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U 0.9794 SSRF BL17U
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 50 98.4 19690 19381
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.07 86.5
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 4JAK 2 49.12 18237 983 99.61 0.2136 0.21191 0.2122 0.24544 0.2426 RANDOM 39.483
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] 1.45 0.08 -0.16 -1.27
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.318 r_dihedral_angle_4_deg 22.344 r_dihedral_angle_3_deg 17.03 r_angle_other_deg 13.364 r_scangle_it 8.101 r_scbond_it 6.296 r_mcangle_it 5.942 r_dihedral_angle_1_deg 5.163 r_mcbond_it 4.399 r_bond_other_d 3.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.318 r_dihedral_angle_4_deg 22.344 r_dihedral_angle_3_deg 17.03 r_angle_other_deg 13.364 r_scangle_it 8.101 r_scbond_it 6.296 r_mcangle_it 5.942 r_dihedral_angle_1_deg 5.163 r_mcbond_it 4.399 r_bond_other_d 3.31 r_angle_refined_deg 1.24 r_chiral_restr 0.079 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined 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 2462 Nucleic Acid Atoms Solvent Atoms 48 Heterogen Atoms 75
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling