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Ligand-free structure of the GrpU microcompartment shell protein from Pectobacterium wasabiae
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 296 0.1M sodium/potassium phosphate, 30% 2-methyl-2,4-pentanediol, pH 6.0, vapor diffusion, hanging drop, temperature 296K
Crystal Properties Matthews coefficient Solvent content 2.1 41.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 117.845 α = 90 b = 117.845 β = 90 c = 76.023 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 2012-03-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 0.97920 APS 24-ID-C
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 2.79 100 99.5 0.087 10.2 12.9 9715
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 2.79 2.9 97.5 0.602 6.1 937
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.79 60.97 9710 468 99.35 0.2178 0.2154 0.218 0.2671 0.2743 RANDOM 99.336
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] -3.65 -1.83 -3.65 11.86
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.611 r_dihedral_angle_3_deg 19.281 r_dihedral_angle_4_deg 18.741 r_mcangle_it 6.947 r_dihedral_angle_1_deg 5.67 r_mcbond_it 4.506 r_mcbond_other 4.505 r_angle_refined_deg 1.602 r_angle_other_deg 1.446 r_chiral_restr 0.091
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.611 r_dihedral_angle_3_deg 19.281 r_dihedral_angle_4_deg 18.741 r_mcangle_it 6.947 r_dihedral_angle_1_deg 5.67 r_mcbond_it 4.506 r_mcbond_other 4.505 r_angle_refined_deg 1.602 r_angle_other_deg 1.446 r_chiral_restr 0.091 r_bond_refined_d 0.011 r_bond_other_d 0.007 r_gen_planes_refined 0.007 r_gen_planes_other 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2637 Nucleic Acid Atoms Solvent Atoms 4 Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction