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X-ray structure of the 3,4-ketoisomerase domain of FdtD from Shewanella denitrificans
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4MZU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 292 16-18% PEG 8000, 200 mM NaCl, 100 mM MOPS
Crystal Properties Matthews coefficient Solvent content 2.81 56.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.405 α = 90 b = 64.579 β = 111.39 c = 112.968 γ = 90
Symmetry Space Group P 1 21 1
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 Bruker Platinum 135 2014-10-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200 1.5418
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 1.7 30 91.8 0.052 0.052 46.4 3.3 115507 115507
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 1.7 1.76 82.4 0.132 6.2 2.1
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 4MZU 1.7 28.28 109726 5776 91.74 0.17291 0.17112 0.1784 0.20733 0.2136 RANDOM 28.133
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] 1.25 -1.37 -0.59 -0.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.223 r_dihedral_angle_4_deg 26.246 r_dihedral_angle_3_deg 15.304 r_dihedral_angle_1_deg 7.352 r_angle_refined_deg 1.937 r_angle_other_deg 0.821 r_chiral_restr 0.124 r_bond_refined_d 0.013 r_gen_planes_refined 0.011 r_gen_planes_other 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.223 r_dihedral_angle_4_deg 26.246 r_dihedral_angle_3_deg 15.304 r_dihedral_angle_1_deg 7.352 r_angle_refined_deg 1.937 r_angle_other_deg 0.821 r_chiral_restr 0.124 r_bond_refined_d 0.013 r_gen_planes_refined 0.011 r_gen_planes_other 0.001 r_bond_other_d 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_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7043 Nucleic Acid Atoms Solvent Atoms 749 Heterogen Atoms 148
Software Software Software Name Purpose REFMAC refinement SAINT data reduction SADABS data scaling PHASER phasing