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Crystal structure of DotM cytoplasmic domain (residues 153-380), double mutant R196E/R197E
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 lithium sulphate
0.1 M MES pH 6.0
20% w/v PEG 4000
Crystal Properties Matthews coefficient Solvent content 2.55 51.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 118.466 α = 90 b = 118.466 β = 90 c = 66.471 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 PIXEL DECTRIS PILATUS 6M-F 2016-07-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 0.979 Diamond I02
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 1.79 66.47 100 0.168 12 6.6 50188
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 1.79 1.82 100 0.046 0.672 2.6 6.5
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 1.79 66.47 47264 2452 99.13 0.20508 0.20254 0.2121 0.2538 0.2575 RANDOM 35.269
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] 1.15 0.57 1.15 -3.72
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.645 r_dihedral_angle_4_deg 16.684 r_dihedral_angle_3_deg 15.098 r_long_range_B_refined 10.709 r_long_range_B_other 10.422 r_scangle_other 6.246 r_dihedral_angle_1_deg 6.064 r_mcangle_it 4.558 r_mcangle_other 4.557 r_scbond_it 4.367
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.645 r_dihedral_angle_4_deg 16.684 r_dihedral_angle_3_deg 15.098 r_long_range_B_refined 10.709 r_long_range_B_other 10.422 r_scangle_other 6.246 r_dihedral_angle_1_deg 6.064 r_mcangle_it 4.558 r_mcangle_other 4.557 r_scbond_it 4.367 r_scbond_other 4.091 r_mcbond_it 3.16 r_mcbond_other 3.16 r_angle_refined_deg 1.955 r_angle_other_deg 1.138 r_chiral_restr 0.12 r_bond_refined_d 0.019 r_gen_planes_refined 0.01 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 3530 Nucleic Acid Atoms Solvent Atoms 345 Heterogen Atoms 50
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling PHASER phasing