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Crystal structure of a 5-keto-2-deoxygluconokinase (NCgl0155, Cgl0158) from Corynebacterium glutamicum ATCC 13032 KITASATO at 1.89 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2QCV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.6 293 0.200M NH4OAc, 30.00% PEG-4000, 0.1M Citrate pH 5.6, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.07 40.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.908 α = 101.86 b = 79.494 β = 95.72 c = 81.703 γ = 92.11
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 MARMOSAIC 300 mm CCD 2008-10-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-B APS 23-ID-B
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 1.89 37.804 97.1 0.065 7.8 2.3 87262 87262 25.396
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.89 1.94 95.8 0.438 0.438 1.2 2 6386
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2QCV 1.89 37.804 87222 4384 96.98 0.1828 0.1805 0.2252 0.2438 RANDOM 37.5491
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] 0.23 0.42 0.14 -0.49 0.53 0.54
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.535 r_dihedral_angle_4_deg 14.737 r_dihedral_angle_3_deg 14.591 r_dihedral_angle_1_deg 6.691 r_scangle_it 3.121 r_scbond_it 1.938 r_angle_refined_deg 1.574 r_angle_other_deg 1.327 r_mcangle_it 1.211 r_mcbond_it 0.681
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.535 r_dihedral_angle_4_deg 14.737 r_dihedral_angle_3_deg 14.591 r_dihedral_angle_1_deg 6.691 r_scangle_it 3.121 r_scbond_it 1.938 r_angle_refined_deg 1.574 r_angle_other_deg 1.327 r_mcangle_it 1.211 r_mcbond_it 0.681 r_mcbond_other 0.182 r_chiral_restr 0.091 r_bond_refined_d 0.016 r_gen_planes_refined 0.007 r_bond_other_d 0.003 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9480 Nucleic Acid Atoms Solvent Atoms 577 Heterogen Atoms 13
Software Software Software Name Purpose REFMAC refinement SCALA data scaling PDB_EXTRACT data extraction MOSFLM data reduction MOLREP phasing