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Crystal structure of DotM cytoplasmic domain (residues 153-380),R217E
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6EXB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 289 0.2 M potassium iodide
0.1 M MES pH 6.5
25% w/v PEG 4000
Crystal Properties Matthews coefficient Solvent content 2.59 52.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 118.278 α = 90 b = 118.278 β = 90 c = 66.571 γ = 120
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 ADSC QUANTUM 315r 2016-10-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.976 ESRF ID23-1
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 53.45 99.6 0.181 7.88 6.7 34191
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.05 99.2 2.44 0.623 1.5 6.8
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 6EXB 2 53.45 34191 1749 99.44 0.2251 0.22301 0.2293 0.26444 0.2697 RANDOM 44.709
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] 1.1 0.55 1.1 -3.57
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.189 r_dihedral_angle_3_deg 17.709 r_dihedral_angle_4_deg 13.789 r_long_range_B_refined 9.239 r_long_range_B_other 9.21 r_scangle_other 6.956 r_dihedral_angle_1_deg 6.636 r_mcangle_it 5.297 r_mcangle_other 5.295 r_scbond_it 4.562
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.189 r_dihedral_angle_3_deg 17.709 r_dihedral_angle_4_deg 13.789 r_long_range_B_refined 9.239 r_long_range_B_other 9.21 r_scangle_other 6.956 r_dihedral_angle_1_deg 6.636 r_mcangle_it 5.297 r_mcangle_other 5.295 r_scbond_it 4.562 r_scbond_other 4.562 r_mcbond_it 3.514 r_mcbond_other 3.511 r_angle_refined_deg 1.914 r_angle_other_deg 1.11 r_chiral_restr 0.11 r_bond_refined_d 0.017 r_gen_planes_refined 0.008 r_bond_other_d 0.003 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 3540 Nucleic Acid Atoms Solvent Atoms 134 Heterogen Atoms 42
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing