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Crystal structure of Gluconate 5-dehydrogenase (TM0441) from Thermotoga maritima at 2.07 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1G6K
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION,SITTING DROP,NANODROP 4.2 277 Acetate pH 4.2, 35% Glycerol, 0.4M NH4H2PO3 , VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 3.89 68.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 123.504 α = 90 b = 123.504 β = 90 c = 122.323 γ = 90
Symmetry Space Group P 43 21 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 APS water cooled; sagitally focusing 2nd crystal, Rosenbaum-Rock vertical focusing mirror 2004-02-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-BM APS 19-BM
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.96 50 89.42 0.088 16.01 6.89 61222 32.51
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.96 2.03 72.83 0.672 1.06 2.35 4917
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 1g6k 2.07 43.67 50440 2715 91.5 0.15148 0.14999 0.1631 0.17955 0.1879 RANDOM 26.843
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] -1.08 -1.08 2.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.122 r_dihedral_angle_4_deg 14.893 r_dihedral_angle_3_deg 13.495 r_scangle_it 6.908 r_dihedral_angle_1_deg 5.97 r_scbond_it 5.163 r_mcangle_it 2.492 r_mcbond_it 2.181 r_angle_refined_deg 1.655 r_angle_other_deg 0.947
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.122 r_dihedral_angle_4_deg 14.893 r_dihedral_angle_3_deg 13.495 r_scangle_it 6.908 r_dihedral_angle_1_deg 5.97 r_scbond_it 5.163 r_mcangle_it 2.492 r_mcbond_it 2.181 r_angle_refined_deg 1.655 r_angle_other_deg 0.947 r_mcbond_other 0.521 r_nbd_refined 0.203 r_symmetry_vdw_other 0.197 r_nbd_other 0.176 r_nbtor_refined 0.175 r_symmetry_hbond_refined 0.159 r_symmetry_vdw_refined 0.146 r_xyhbond_nbd_refined 0.132 r_chiral_restr 0.097 r_nbtor_other 0.085 r_bond_refined_d 0.018 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3838 Nucleic Acid Atoms Solvent Atoms 331 Heterogen Atoms 102
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MOLREP phasing REFMAC refinement