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Crystal structure of 2-keto-3-deoxy-D-gluconate dehydrogenase from Streptococcus agalactiae
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3CXR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 20% polyethylene glycol monomethyl ether 550, 0.1 M sodium chloride, and 0.1 M sodium N,N-bis(2-hydroxyethyl)glycine (pH 9.0)
Crystal Properties Matthews coefficient Solvent content 3.08 60.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.943 α = 90 b = 83.943 β = 90 c = 181.101 γ = 120
Symmetry Space Group P 62 2 2
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 315 2011-02-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL38B1 1 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 2.9 50 99.8 78.5 22.5 8964
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 3cxr 2.9 35.64 8454 421 99.2 0.21477 0.21139 0.2116 0.2869 0.2911 RANDOM 75.396
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] 31.64 31.64 -63.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.806 r_dihedral_angle_3_deg 20.537 r_dihedral_angle_4_deg 18.552 r_long_range_B_refined 8.874 r_long_range_B_other 8.873 r_dihedral_angle_1_deg 6.056 r_mcangle_other 5.633 r_mcangle_it 5.626 r_scangle_other 5.486 r_mcbond_it 3.545
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.806 r_dihedral_angle_3_deg 20.537 r_dihedral_angle_4_deg 18.552 r_long_range_B_refined 8.874 r_long_range_B_other 8.873 r_dihedral_angle_1_deg 6.056 r_mcangle_other 5.633 r_mcangle_it 5.626 r_scangle_other 5.486 r_mcbond_it 3.545 r_mcbond_other 3.468 r_scbond_it 3.351 r_scbond_other 3.35 r_angle_refined_deg 1.219 r_angle_other_deg 0.779 r_chiral_restr 0.065 r_bond_refined_d 0.008 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 1992 Nucleic Acid Atoms Solvent Atoms 5 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement