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Crystal structure of the short chain dehydrogenase Galactitol- Dehydrogenase (GatDH) of Rhodobacter sphaeroides in complex with NAD+ and 1,2-Pentandiol
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 5.5 100MM MES PH 5.5, 200MM MAGNESIUM CHLORIDE, 12.5%(W/V)MPEG5000
Crystal Properties Matthews coefficient Solvent content 2.1 41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.72 α = 90 b = 113.62 β = 90 c = 256.925 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 MARRESEARCH MIRRORS 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) 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 1.95 20 98.5 0.127 15.1 8.9 64019 1.8 23.51
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.95 2.06 94.9 0.691 1.8 4.8
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT SWISS PROT MODEL 1.95 19.86 60703 3240 98.38 0.189 0.187 0.1848 0.24 0.1827 RANDOM 27.368
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] 0.01 0.01 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.156 r_dihedral_angle_4_deg 19.792 r_dihedral_angle_3_deg 15.447 r_dihedral_angle_1_deg 6.141 r_angle_refined_deg 1.69 r_angle_other_deg 1.199 r_symmetry_hbond_refined 0.779 r_symmetry_vdw_other 0.282 r_nbd_other 0.21 r_nbd_refined 0.205
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.156 r_dihedral_angle_4_deg 19.792 r_dihedral_angle_3_deg 15.447 r_dihedral_angle_1_deg 6.141 r_angle_refined_deg 1.69 r_angle_other_deg 1.199 r_symmetry_hbond_refined 0.779 r_symmetry_vdw_other 0.282 r_nbd_other 0.21 r_nbd_refined 0.205 r_symmetry_vdw_refined 0.204 r_nbtor_refined 0.17 r_xyhbond_nbd_refined 0.168 r_chiral_restr 0.104 r_nbtor_other 0.092 r_bond_refined_d 0.017 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7386 Nucleic Acid Atoms Solvent Atoms 495 Heterogen Atoms 215
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing