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Crystal structure of the short-chain dehydrogenase Galactitol-Dehydrogenase (GatDH) of Rhodobacter sphaeroides in complex with NAD and erythritol
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model SwissModel SWISS PROT MODEL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.7 291 100MM MES, 200MM MAGNESIUMCHLORIDE, 14.0%(W/V)MPEG5000, pH 5.7, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.12 41.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.863 α = 90 b = 113.838 β = 90 c = 123.234 γ = 90
Symmetry Space Group P 21 21 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 RAYONIX MIRRORS 2008-10-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.2 BESSY 14.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.8 30 99.9 0.078 0.078 17.65 7.3 83822 83822 28.474
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) 1.8 1.85 99.3 0.68 0.68 2.96 6.8 6087
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 SWISS PROT MODEL 1.8 30 79631 79631 4191 100 0.1861 0.1861 0.18419 0.1865 0.22267 0.2257 RANDOM 24.924
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 2.36 -1.87
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.583 r_dihedral_angle_4_deg 17.487 r_dihedral_angle_3_deg 15.112 r_dihedral_angle_1_deg 5.96 r_scangle_it 3.24 r_scbond_it 2.062 r_angle_refined_deg 1.389 r_mcangle_it 1.331 r_mcbond_it 0.787 r_chiral_restr 0.093
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.583 r_dihedral_angle_4_deg 17.487 r_dihedral_angle_3_deg 15.112 r_dihedral_angle_1_deg 5.96 r_scangle_it 3.24 r_scbond_it 2.062 r_angle_refined_deg 1.389 r_mcangle_it 1.331 r_mcbond_it 0.787 r_chiral_restr 0.093 r_bond_refined_d 0.014 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7392 Nucleic Acid Atoms Solvent Atoms 509 Heterogen Atoms 210
Software Software Software Name Purpose MOLREP phasing REFMAC refinement XDS data reduction XDS data scaling