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Structure of E. coli 5-Methyluridine Methyltransferase TrmA in complex with 19 nucleotide T-arm analogue
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2BH2 PDB entry 2BH2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.4 295 100 mM sodium cacodylate pH 7.4, 200 mM sodium sulfate, and 22 % PEG-8000, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 3.1 60.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 184.407 α = 90 b = 70.131 β = 120.88 c = 107.95 γ = 90
Symmetry Space Group C 1 2 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 315r 2007-01-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.3.1 1.11 ALS 8.3.1
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 2.43 35.1 0.078 5.7 2.2 90859 42023 2 2
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 2.43 2.49 83.7 0.27 1.7 2
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 SAD THROUGHOUT PDB entry 2BH2 2.43 35.07 38764 3230 93.62 0.2297 0.22509 0.2268 0.28635 0.2898 RANDOM 47.563
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] -0.02 -0.01 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.587 r_dihedral_angle_3_deg 20.099 r_dihedral_angle_4_deg 15.169 r_dihedral_angle_1_deg 6.715 r_scangle_it 3.392 r_scbond_it 2.102 r_angle_refined_deg 1.781 r_mcangle_it 1.453 r_angle_other_deg 1.434 r_mcbond_it 0.78
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.587 r_dihedral_angle_3_deg 20.099 r_dihedral_angle_4_deg 15.169 r_dihedral_angle_1_deg 6.715 r_scangle_it 3.392 r_scbond_it 2.102 r_angle_refined_deg 1.781 r_mcangle_it 1.453 r_angle_other_deg 1.434 r_mcbond_it 0.78 r_symmetry_hbond_refined 0.275 r_symmetry_vdw_other 0.25 r_xyhbond_nbd_refined 0.213 r_mcbond_other 0.143 r_symmetry_vdw_refined 0.135 r_chiral_restr 0.085 r_bond_refined_d 0.016 r_gen_planes_refined 0.007 r_xyhbond_nbd_other 0.007 r_gen_planes_other 0.003 r_bond_other_d 0.002 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5914 Nucleic Acid Atoms 804 Solvent Atoms 261 Heterogen Atoms
Software Software Software Name Purpose MOSFLM data reduction SOLVE phasing DM phasing REFMAC refinement PDB_EXTRACT data extraction ADSC data collection SCALA data scaling