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Crystal structure of Pectobacterium carotovorum 2-keto-3-deoxy-D-gluconate dehydrogenase complexed with NAD+
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4Z9Y
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 PEG 4000, isopropanol, nicotinamide adenine dinucleotide
Crystal Properties Matthews coefficient Solvent content 2.26 45.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.663 α = 90 b = 72.654 β = 90.81 c = 98.991 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 RIGAKU JUPITER 210 2011-07-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL38B1 1.0000 SPring-8 BL38B1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.55 50 99.7 40.5 4.1 140618
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.55 1.58 99.9 4.4 4.1
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 4Z9Y 1.55 34.13 133535 7048 99.63 0.20042 0.19909 0.2071 0.22581 0.2337 RANDOM 24.487
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] -0.04 0.36 0.07 -0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.652 r_dihedral_angle_4_deg 16.037 r_dihedral_angle_3_deg 11.976 r_dihedral_angle_1_deg 5.616 r_long_range_B_refined 3.751 r_long_range_B_other 3.751 r_scangle_other 2.048 r_mcangle_it 1.634 r_mcangle_other 1.634 r_scbond_it 1.268
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.652 r_dihedral_angle_4_deg 16.037 r_dihedral_angle_3_deg 11.976 r_dihedral_angle_1_deg 5.616 r_long_range_B_refined 3.751 r_long_range_B_other 3.751 r_scangle_other 2.048 r_mcangle_it 1.634 r_mcangle_other 1.634 r_scbond_it 1.268 r_scbond_other 1.267 r_angle_refined_deg 1.167 r_mcbond_it 1.035 r_mcbond_other 1.035 r_angle_other_deg 0.735 r_chiral_restr 0.067 r_bond_refined_d 0.007 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7374 Nucleic Acid Atoms Solvent Atoms 596 Heterogen Atoms 44
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling SCALEPACK data reduction MOLREP phasing