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Crystal structure of the PduU shell protein from the Pdu microcompartment
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2EWH PDB entry 2EWH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 298 50 mM HEPES, 300 mM LiSO4, 20% PEG-3350, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal Properties Matthews coefficient Solvent content 2.13 42.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.14 α = 90 b = 74.14 β = 90 c = 218.021 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 CCD ADSC QUANTUM 315 2007-04-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.2 1.000 ALS 8.2.2
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 1.8 90 99.2 0.159 9 5 40948
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 1.8 1.86 93.5 0.505 3.8 3859
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 PDB entry 2EWH 1.8 61.59 40944 2063 99.09 0.205 0.203 0.2089 0.242 0.2469 RANDOM 23.646
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] -2.55 -1.27 -2.55 3.82
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.27 r_dihedral_angle_3_deg 11.858 r_dihedral_angle_4_deg 10.075 r_dihedral_angle_1_deg 5.413 r_scangle_it 3.334 r_mcangle_it 3.012 r_mcbond_it 2.657 r_scbond_it 2.433 r_angle_refined_deg 1.431 r_angle_other_deg 0.905
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.27 r_dihedral_angle_3_deg 11.858 r_dihedral_angle_4_deg 10.075 r_dihedral_angle_1_deg 5.413 r_scangle_it 3.334 r_mcangle_it 3.012 r_mcbond_it 2.657 r_scbond_it 2.433 r_angle_refined_deg 1.431 r_angle_other_deg 0.905 r_mcbond_other 0.714 r_symmetry_vdw_other 0.297 r_symmetry_hbond_refined 0.206 r_nbd_refined 0.197 r_symmetry_vdw_refined 0.192 r_nbd_other 0.183 r_nbtor_refined 0.171 r_xyhbond_nbd_refined 0.154 r_nbtor_other 0.086 r_chiral_restr 0.085 r_bond_refined_d 0.012 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3458 Nucleic Acid Atoms Solvent Atoms 165 Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction BOS data collection