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Crystal structure of PduT a trimeric bacterial microcompartment protein with 4Fe-4S cluster binding site
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 292 0.1M NaCl, 0.1M Bicine, 25% PEG 550, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 292.0K
Crystal Properties Matthews coefficient Solvent content 1.93 36.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.68 α = 90 b = 67.68 β = 90 c = 62.03 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 210 2009-10-30 M SINGLE WAVELENGTH 2 1 x-ray 100 CCD ADSC QUANTUM 315 2010-07-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 0.933 ESRF ID14-1 2 SYNCHROTRON DIAMOND BEAMLINE I04 1.1410 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 1,2 1.86 33.84 100 0.035 0.095 18.5 8.2 13647 13647 21.2
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) 1.86 1.96 98 0.22 0.58 3.7 8 1979
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (All) 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 SAD THROUGHOUT 1.86 29.71 13647 12258 1372 99.96 0.20394 0.19862 0.1972 0.2515 0.2507 RANDOM 25.825
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.079 r_dihedral_angle_3_deg 19.148 r_dihedral_angle_4_deg 14.685 r_dihedral_angle_1_deg 6.358 r_scangle_it 6.323 r_scbond_it 4.03 r_mcangle_it 2.391 r_angle_refined_deg 2.068 r_mcbond_it 1.381 r_chiral_restr 0.137
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.079 r_dihedral_angle_3_deg 19.148 r_dihedral_angle_4_deg 14.685 r_dihedral_angle_1_deg 6.358 r_scangle_it 6.323 r_scbond_it 4.03 r_mcangle_it 2.391 r_angle_refined_deg 2.068 r_mcbond_it 1.381 r_chiral_restr 0.137 r_bond_refined_d 0.023 r_gen_planes_refined 0.01 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 1317 Nucleic Acid Atoms Solvent Atoms 38 Heterogen Atoms
Software Software Software Name Purpose ADSC data collection PHENIX model building REFMAC refinement MOSFLM data reduction SCALA data scaling PHENIX phasing