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Structure of [FeS]cluster-free Apo Form of 6-Phosphogluconate Dehydratase from Shewanella oneidensis
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 295 5% PEG400, 50mM cacodylate, 3mM DTT, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.15 42.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.364 α = 90 b = 118.649 β = 90 c = 160.017 γ = 90
Symmetry Space Group P 21 21 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 MARMOSAIC 225 mm CCD 2004-12-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 0.9792 APS 22-ID
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 2.49 50 99.8 0.08 0.08 15.1 9.8 41534 41534 1 1
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 2.49 2.59 99.8 0.206 0.206 8.6 4092
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 (All) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION SAD THROUGHOUT 2.49 48.68 39386 39386 2086 100 0.2325 0.2325 0.2295 0.2908 0.2839 RANDOM 29.211
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] 0.91 0.45 -1.36
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.218 r_dihedral_angle_4_deg 18.402 r_dihedral_angle_3_deg 16.609 r_dihedral_angle_1_deg 4.863 r_scangle_it 1.675 r_scbond_it 1.146 r_angle_refined_deg 1.1 r_mcangle_it 0.801 r_mcbond_it 0.537 r_nbtor_refined 0.295
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.218 r_dihedral_angle_4_deg 18.402 r_dihedral_angle_3_deg 16.609 r_dihedral_angle_1_deg 4.863 r_scangle_it 1.675 r_scbond_it 1.146 r_angle_refined_deg 1.1 r_mcangle_it 0.801 r_mcbond_it 0.537 r_nbtor_refined 0.295 r_symmetry_vdw_refined 0.208 r_nbd_refined 0.195 r_xyhbond_nbd_refined 0.132 r_symmetry_hbond_refined 0.132 r_chiral_restr 0.069 r_bond_refined_d 0.007 r_gen_planes_refined 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7563 Nucleic Acid Atoms Solvent Atoms 553 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement DENZO data reduction HKL-2000 data scaling SOLVE phasing