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X-ray structure of the KijD1 C3-methyltransfeerase, converted to monomeric form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5T64
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 9 293 18-22% PEG-3350, 2%MPD, 100 mM MES, 10 mM TDP, 5 mM SAH
Crystal Properties Matthews coefficient Solvent content 1.94 36.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.707 α = 96.05 b = 82.455 β = 110.7 c = 82.825 γ = 112.09
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 2015-12-12 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 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 75 96.6 0.074 7.3 3.1 90291
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 91 0.305 2.1 1.8
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 5T64 2 30 85763 4528 96.6 0.17855 0.17556 0.1841 0.23424 0.2391 RANDOM 25.19
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] -0.72 -0.11 0.09 0.45 0.6 -0.33
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.969 r_dihedral_angle_4_deg 18.325 r_dihedral_angle_3_deg 15.553 r_dihedral_angle_1_deg 6.659 r_long_range_B_refined 5.44 r_long_range_B_other 5.439 r_scangle_other 3.817 r_mcangle_it 2.961 r_mcangle_other 2.961 r_scbond_it 2.389
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.969 r_dihedral_angle_4_deg 18.325 r_dihedral_angle_3_deg 15.553 r_dihedral_angle_1_deg 6.659 r_long_range_B_refined 5.44 r_long_range_B_other 5.439 r_scangle_other 3.817 r_mcangle_it 2.961 r_mcangle_other 2.961 r_scbond_it 2.389 r_scbond_other 2.368 r_mcbond_it 1.879 r_mcbond_other 1.879 r_angle_refined_deg 1.773 r_angle_other_deg 1.038 r_chiral_restr 0.099 r_bond_refined_d 0.014 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.002 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 12428 Nucleic Acid Atoms Solvent Atoms 737 Heterogen Atoms 216
Software Software Software Name Purpose REFMAC refinement SAINT data reduction SADABS data scaling PHASER phasing