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Crystal Structure of E.coli MnmG (GidA), a Highly-Conserved tRNA Modifying Enzyme
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 294 PEG 8000, Sodium Formate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Crystal Properties Matthews coefficient Solvent content 3.04 59.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.904 α = 90 b = 144.326 β = 106.63 c = 147.745 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 2006-02-28 M SINGLE WAVELENGTH 2 1
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 31-ID 0.9798 APS 31-ID 2 SYNCHROTRON NSLS BEAMLINE X12B 0.9793 NSLS X12B
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 2.412 141.42 99.6 0.115 11.6 3.1 133967 129226
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 SAD THROUGHOUT 2.412 141.42 129226 6511 97.41 0.203 0.201 0.238 0.2492 RANDOM 52.284
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] 0.53 -0.3 -1.82 1.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.166 r_dihedral_angle_4_deg 19.937 r_dihedral_angle_3_deg 18.397 r_dihedral_angle_1_deg 6.796 r_scangle_it 3.211 r_scbond_it 1.991 r_angle_refined_deg 1.534 r_mcangle_it 1.381 r_mcbond_it 0.801 r_nbtor_refined 0.299
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.166 r_dihedral_angle_4_deg 19.937 r_dihedral_angle_3_deg 18.397 r_dihedral_angle_1_deg 6.796 r_scangle_it 3.211 r_scbond_it 1.991 r_angle_refined_deg 1.534 r_mcangle_it 1.381 r_mcbond_it 0.801 r_nbtor_refined 0.299 r_symmetry_vdw_refined 0.273 r_symmetry_hbond_refined 0.244 r_nbd_refined 0.216 r_xyhbond_nbd_refined 0.161 r_chiral_restr 0.117 r_bond_refined_d 0.013 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 15637 Nucleic Acid Atoms Solvent Atoms 332 Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling SHARP phasing RESOLVE phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling