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Crystal structure of 2-keto-3-deoxy-D-gluconate dehydrogenase from Pectobacterium carotovorum
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2UVD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 PEG 8000, glycerol, potassium chloride
Crystal Properties Matthews coefficient Solvent content 2.27 45.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.728 α = 90 b = 72.655 β = 90.81 c = 99.048 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 2011-10-22 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) 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 1.63 50 99.6 0.058 39.1 4.1 122189
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 1.63 1.69 98 0.255 0.083 4
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 2UVD 1.63 40.95 115520 6106 99.62 0.17302 0.17167 0.1821 0.19869 0.2082 RANDOM 19.493
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] -0.24 0.22 0.79 -0.55
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.995 r_dihedral_angle_4_deg 16.352 r_dihedral_angle_3_deg 11.227 r_dihedral_angle_1_deg 5.52 r_long_range_B_refined 4.365 r_long_range_B_other 3.991 r_scangle_other 1.718 r_mcangle_it 1.367 r_mcangle_other 1.367 r_angle_refined_deg 1.112
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.995 r_dihedral_angle_4_deg 16.352 r_dihedral_angle_3_deg 11.227 r_dihedral_angle_1_deg 5.52 r_long_range_B_refined 4.365 r_long_range_B_other 3.991 r_scangle_other 1.718 r_mcangle_it 1.367 r_mcangle_other 1.367 r_angle_refined_deg 1.112 r_scbond_it 1.047 r_scbond_other 1.038 r_mcbond_it 0.808 r_mcbond_other 0.808 r_angle_other_deg 0.725 r_chiral_restr 0.066 r_bond_refined_d 0.006 r_gen_planes_refined 0.004 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 7644 Nucleic Acid Atoms Solvent Atoms 925 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling SCALEPACK data reduction MOLREP phasing