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Crystal structure of D-mannonate dehydratase from Novosphingobium aromaticivorans complexed with Mg and 2-keto-3-deoxy-D-gluconate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2QJJ PDB entry 2QJJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 293 25% PEG 3350, 0.1M Tris, 0.2M ammonium sulfate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0
Crystal Properties Matthews coefficient Solvent content 2.21 44.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 116.269 α = 90 b = 165.241 β = 90 c = 167.039 γ = 90
Symmetry Space Group C 2 2 21
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 4 2006-02-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X4A 0.97915 NSLS X4A
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 2 25 96.9 0.073 104980 104980 17.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 PDB entry 2QJJ 2 24.89 104980 104980 5291 96.9 0.162 0.162 0.162 0.1624 0.191 0.1917 RANDOM 24.6
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] -2.57 -0.35 2.92
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 22.4 c_scangle_it 2.75 c_scbond_it 1.92 c_mcangle_it 1.53 c_angle_deg 1.3 c_mcbond_it 1.09 c_improper_angle_d 0.77 c_bond_d 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12227 Nucleic Acid Atoms Solvent Atoms 849 Heterogen Atoms 52
Software Software Software Name Purpose CNS refinement ADSC data collection DENZO data reduction SCALEPACK data scaling PHASER phasing