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Crystal structure of the K271E mutant of Mannonate dehydratase from Novosphingobium aromaticivorans complexed with Mg and D-mannonate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2QJJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 293 3.0M Sodium chloride, 0.1M Bis-Tris, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Crystal Properties Matthews coefficient Solvent content 2.21 44.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 116.254 α = 90 b = 165.312 β = 90 c = 166.853 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 2.2 25 96.1 0.059 78216 78216 20.7
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 2QJJ 2.2 25 78216 78216 3938 96.1 0.168 0.168 0.168 0.1685 0.206 0.2055 RANDOM 28.6
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] -2.26 -0.24 2.5
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 22.2 c_scangle_it 3.04 c_scbond_it 2.1 c_mcangle_it 1.76 c_angle_deg 1.3 c_mcbond_it 1.17 c_improper_angle_d 0.77 c_bond_d 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12222 Nucleic Acid Atoms Solvent Atoms 645 Heterogen Atoms 56
Software Software Software Name Purpose CNS refinement ADSC data collection DENZO data reduction SCALEPACK data scaling PHASER phasing