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X-ray structure of the sugar N-methyltransferase KedS8 from Streptoalloteichus sp ATCC 53650
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3BXO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 277 28-33% MPD, 2.5 mM SAH, 100 mM MOPS
Crystal Properties Matthews coefficient Solvent content 3 58.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.254 α = 90 b = 81.004 β = 90 c = 126.916 γ = 90
Symmetry Space Group I 2 2 2
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 Bruker Platinum 135 2015-05-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 30 97.6 0.045 0.045 14.3 3.4 21803 21803
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 2.1 94 0.143 4.2 2.2
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 MOLECULAR REPLACEMENT THROUGHOUT 3bxo 2 28.71 20689 1114 97.09 0.17062 0.1678 0.1764 0.22577 0.2328 RANDOM 28.478
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] -1.2 0.31 0.89
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.47 r_dihedral_angle_4_deg 21.492 r_dihedral_angle_3_deg 14.893 r_dihedral_angle_1_deg 7.216 r_angle_refined_deg 1.95 r_angle_other_deg 0.841 r_chiral_restr 0.125 r_bond_refined_d 0.012 r_gen_planes_refined 0.009 r_bond_other_d
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.47 r_dihedral_angle_4_deg 21.492 r_dihedral_angle_3_deg 14.893 r_dihedral_angle_1_deg 7.216 r_angle_refined_deg 1.95 r_angle_other_deg 0.841 r_chiral_restr 0.125 r_bond_refined_d 0.012 r_gen_planes_refined 0.009 r_bond_other_d r_gen_planes_other 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_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1885 Nucleic Acid Atoms Solvent Atoms 162 Heterogen Atoms 59
Software Software Software Name Purpose REFMAC refinement SAINT data reduction SADABS data scaling PHASER phasing