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Crystal Structure of rRNA methyltransferase from Sinorhizobium meliloti
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 300 5mM Cobalt chloride , 5mM Magnesium chloride hexahydrate, 0.1M HEPES pH 7.5, 9%(wt/vol) polyethylene glycol 3,350
Crystal Properties Matthews coefficient Solvent content 2.47 50.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.82 α = 90 b = 84.302 β = 90 c = 112.045 γ = 90
Symmetry Space Group P 21 21 21
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 MAR CCD 165 mm 2015-11-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 0.987 ESRF BM14
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) 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 2.28 67.36 98 0.919 46.98 7.9 28693
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION SAD THROUGHOUT 2.28 67.36 26732 1386 96 0.20867 0.20615 0.2127 0.25863 0.2647 RANDOM 38.78
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] -0.39 1.21 -0.82
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.225 r_dihedral_angle_3_deg 18.235 r_dihedral_angle_4_deg 15.165 r_dihedral_angle_1_deg 7.36 r_long_range_B_refined 5.717 r_long_range_B_other 5.717 r_scangle_other 4.112 r_mcangle_it 3.519 r_mcangle_other 3.519 r_scbond_it 2.498
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.225 r_dihedral_angle_3_deg 18.235 r_dihedral_angle_4_deg 15.165 r_dihedral_angle_1_deg 7.36 r_long_range_B_refined 5.717 r_long_range_B_other 5.717 r_scangle_other 4.112 r_mcangle_it 3.519 r_mcangle_other 3.519 r_scbond_it 2.498 r_scbond_other 2.483 r_mcbond_it 2.084 r_mcbond_other 2.082 r_angle_refined_deg 2.075 r_angle_other_deg 1.123 r_chiral_restr 0.116 r_bond_refined_d 0.022 r_gen_planes_refined 0.01 r_bond_other_d 0.002 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3917 Nucleic Acid Atoms Solvent Atoms 37 Heterogen Atoms 12
Software Software Software Name Purpose HKL-3000 data processing SHELXDE phasing REFMAC refinement