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Protein structure of type III plasmid segregation TubR mutant
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3M8E
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 10% PEG 8000, 100 mM HEPES pH 7.5, 8% ethylene glycol , VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.33 47.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 104.4 α = 90 b = 79.518 β = 102.06 c = 32.351 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE RIGAKU RAXIS HTC 2009-06-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E SUPERBRIGHT 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.8 39.75 88.5 0.045 22.5 3.7 6408 5671 3
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) 2.8 2.95 86.4 0.382 2.6 3.6
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 3M8E 2.8 31.37 5393 274 88 0.20696 0.20393 0.2004 0.2661 0.2535 RANDOM 26.684
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] 0.07 -0.17 -0.74 0.6
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.065 r_dihedral_angle_3_deg 20.864 r_dihedral_angle_4_deg 17.019 r_dihedral_angle_1_deg 5.71 r_scangle_it 1.838 r_angle_refined_deg 1.224 r_scbond_it 1.07 r_mcangle_it 0.765 r_mcbond_it 0.392 r_symmetry_vdw_refined 0.314
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.065 r_dihedral_angle_3_deg 20.864 r_dihedral_angle_4_deg 17.019 r_dihedral_angle_1_deg 5.71 r_scangle_it 1.838 r_angle_refined_deg 1.224 r_scbond_it 1.07 r_mcangle_it 0.765 r_mcbond_it 0.392 r_symmetry_vdw_refined 0.314 r_nbtor_refined 0.313 r_nbd_refined 0.236 r_xyhbond_nbd_refined 0.128 r_symmetry_hbond_refined 0.114 r_chiral_restr 0.088 r_bond_refined_d 0.011 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1551 Nucleic Acid Atoms Solvent Atoms 7 Heterogen Atoms
Software Software Software Name Purpose CrystalClear data collection PHASER phasing REFMAC refinement MOSFLM data reduction SCALA data scaling