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RAWV_CTD (Loop Structure) of 16S/23S 2'-O-methyltransferase TlyA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5EOV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 293 8% Tascimate pH 8.0, 20% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.12 42.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.922 α = 90 b = 70.922 β = 90 c = 79.882 γ = 90
Symmetry Space Group P 43 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 80 CCD RAYONIX MX300-HS 2016-04-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1 APS 22-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.9 53.04 99.87 0.121 0.928 45.8 12.8 16678
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 1.97 99.9 0.762 0.928 3.6 9.1
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 5EOV 1.9 53.04 15009 1668 99.87 0.17843 0.17349 0.1833 0.22399 0.2364 RANDOM 42.628
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] 0.17 0.17 -0.35
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.011 r_dihedral_angle_4_deg 15.629 r_dihedral_angle_3_deg 11.806 r_long_range_B_refined 7.388 r_long_range_B_other 7.386 r_dihedral_angle_1_deg 5.672 r_scangle_other 5.475 r_mcangle_other 3.66 r_mcangle_it 3.658 r_scbond_it 3.58
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.011 r_dihedral_angle_4_deg 15.629 r_dihedral_angle_3_deg 11.806 r_long_range_B_refined 7.388 r_long_range_B_other 7.386 r_dihedral_angle_1_deg 5.672 r_scangle_other 5.475 r_mcangle_other 3.66 r_mcangle_it 3.658 r_scbond_it 3.58 r_scbond_other 3.562 r_mcbond_it 2.667 r_mcbond_other 2.623 r_angle_refined_deg 1.526 r_angle_other_deg 0.938 r_chiral_restr 0.092 r_bond_refined_d 0.011 r_gen_planes_refined 0.007 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 1528 Nucleic Acid Atoms Solvent Atoms 45 Heterogen Atoms 6
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHENIX phasing