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Crystal structure of the mutant Y90F of divergent galactarate dehydratase from Oceanobacillus iheyensis complexed with Mg and galactarate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3ES7 PDB entry 3ES7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 293 25% PEG 3350, 0.1M Tris-HCl, 0.2M NaCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Crystal Properties Matthews coefficient Solvent content 2.48 50.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 119.966 α = 90 b = 119.966 β = 90 c = 122.165 γ = 90
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 2009-04-17 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 1.8 25 99.8 0.087 79510 79510 25
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 3ES7 1.8 24.79 79510 79510 3991 99.8 0.195 0.195 0.194 0.1934 0.223 0.2231 RANDOM 29.6
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] 0.49 0.49 -0.98
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 22.9 c_scangle_it 3.03 c_scbond_it 2.06 c_mcangle_it 1.68 c_angle_deg 1.3 c_mcbond_it 1.15 c_improper_angle_d 0.71 c_bond_d 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6192 Nucleic Acid Atoms Solvent Atoms 488 Heterogen Atoms 32
Software Software Software Name Purpose ADSC data collection BALBES phasing CNS refinement DENZO data reduction SCALEPACK data scaling