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Crystal structure of a trimeric bacterial microcompartment shell protein PduB
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4FAY PDB ENTRY 4FAY
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 292K
Crystal Properties Matthews coefficient Solvent content 1.87 34.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.01 α = 90 b = 119.55 β = 90 c = 147.09 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 CCD ADSC QUANTUM 315r 2012-09-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9795 Diamond I04
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 1.64 59.77 99.8 0.131 0.074 0.102 4.9 74480 9.6 9.916
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.64 1.68 99.8 0.703 0.393 2.2 4.9 26795
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 (All) 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 PDB ENTRY 4FAY 1.64 59.77 98878 70684 3749 99.77 0.15519 0.15519 0.15279 0.1565 0.20028 0.2024 RANDOM 11.795
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] -0.02 0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.288 r_dihedral_angle_4_deg 14.812 r_dihedral_angle_3_deg 12.549 r_dihedral_angle_1_deg 6.622 r_scangle_it 5.595 r_scbond_it 3.418 r_angle_refined_deg 1.982 r_mcangle_it 1.92 r_mcbond_it 1.244 r_chiral_restr 0.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.288 r_dihedral_angle_4_deg 14.812 r_dihedral_angle_3_deg 12.549 r_dihedral_angle_1_deg 6.622 r_scangle_it 5.595 r_scbond_it 3.418 r_angle_refined_deg 1.982 r_mcangle_it 1.92 r_mcbond_it 1.244 r_chiral_restr 0.15 r_bond_refined_d 0.025 r_gen_planes_refined 0.011 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 4989 Nucleic Acid Atoms Solvent Atoms 780 Heterogen Atoms
Software Software Software Name Purpose ADSC data collection PHENIX model building REFMAC refinement XDS data reduction SCALA data scaling PHENIX phasing