☰ Navigation Tabs
Crystal structure of the short-chain dehydrogenase Galactitol- Dehydrogenase (GatDH) of Rhodobacter sphaeroides in complex with NAD
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 6.5 4% N-PROPANOLE, 100MM SODIUM CACODYLATE, PH 6.5, 200MM SODIUM ACETATE, 30% PEG 8000
Crystal Properties Matthews coefficient Solvent content 2.71 55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 97.79 α = 90 b = 106.62 β = 90 c = 109.33 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 ADSC CCD M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-2 ESRF ID14-2
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 1.25 19.94 98.6 0.1 8.4 6.7 313700 2 20.5
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 1.25 1.28 92.9 0.56 2 2.5
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT SWISS PROT MODEL 1.25 19.94 313320 15666 99.88 0.13609 0.13393 0.17749 0.1767 RANDOM 21.51
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] 0.09 -0.06 -0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.97 r_sphericity_free 21.107 r_dihedral_angle_4_deg 18.654 r_dihedral_angle_3_deg 12.454 r_sphericity_bonded 9.851 r_scangle_it 8.378 r_scbond_it 6.863 r_dihedral_angle_1_deg 6.314 r_mcangle_it 4.112 r_mcbond_it 3.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.97 r_sphericity_free 21.107 r_dihedral_angle_4_deg 18.654 r_dihedral_angle_3_deg 12.454 r_sphericity_bonded 9.851 r_scangle_it 8.378 r_scbond_it 6.863 r_dihedral_angle_1_deg 6.314 r_mcangle_it 4.112 r_mcbond_it 3.1 r_rigid_bond_restr 3.07 r_angle_refined_deg 2.581 r_symmetry_vdw_refined 0.264 r_symmetry_hbond_refined 0.254 r_chiral_restr 0.168 r_bond_refined_d 0.03 r_gen_planes_refined 0.016 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7392 Nucleic Acid Atoms Solvent Atoms 1765 Heterogen Atoms 210
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing