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Crystal structure of a trimeric bacterial microcompartment shell protein PduB with glycerol metabolites
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3IO0 EtuB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 292 0.1 M sodium cacodylate, 1.4 M sodium acetate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 292.0K
Crystal Properties Matthews coefficient Solvent content 1.89 35.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.865 α = 90 b = 120.864 β = 90 c = 145.531 γ = 90
Symmetry Space Group C 2 2 21
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 2M 2012-04-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.91730 Diamond I04-1
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 1.55 72.78 99 0.088 0.088 11.3 4.5 87436 16
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 1.55 1.64 96.2 0.908 2 4.4 12243
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT EtuB 1.56 72.78 84081 83762 4338 99.62 0.174 0.17263 0.20188 0.1937 RANDOM 18.515
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] 0.01 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.659 r_dihedral_angle_4_deg 14.457 r_dihedral_angle_3_deg 12.593 r_dihedral_angle_1_deg 6.809 r_scangle_it 4.68 r_scbond_it 2.971 r_mcangle_it 1.718 r_angle_refined_deg 1.716 r_mcbond_it 1.102 r_chiral_restr 0.114
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.659 r_dihedral_angle_4_deg 14.457 r_dihedral_angle_3_deg 12.593 r_dihedral_angle_1_deg 6.809 r_scangle_it 4.68 r_scbond_it 2.971 r_mcangle_it 1.718 r_angle_refined_deg 1.716 r_mcbond_it 1.102 r_chiral_restr 0.114 r_bond_refined_d 0.02 r_gen_planes_refined 0.009 r_bond_other_d r_angle_other_deg 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_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4980 Nucleic Acid Atoms Solvent Atoms 401 Heterogen Atoms 106
Software Software Software Name Purpose ADSC data collection PHENIX model building REFMAC refinement XDS data reduction SCALA data scaling PHENIX phasing