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Crystal structure of L-galactose dehydrogenase M212Q mutant in complex with L-glucose and NADP+
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9W7A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 30% (w/v) PEG 8000, 200 mM ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 2.23 44.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.051 α = 90 b = 88.767 β = 90 c = 95.195 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 95 PIXEL DECTRIS EIGER X 4M 2026-02-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-1A 1.000 Photon Factory BL-1A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) 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 1.76 47.6 100 0.998 13.8 13 67918
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.76 1.79 0.764
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 9W7A 1.76 47.6 67846 3359 99.993 0.185 0.1846 0.1923 0.2035 0.2155 16.92
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] -0.051 0.228 -0.177
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.529 r_dihedral_angle_3_deg 11.864 r_dihedral_angle_1_deg 5.319 r_lrange_it 4.558 r_lrange_other 4.519 r_dihedral_angle_2_deg 4.206 r_scangle_it 4.021 r_scangle_other 4.017 r_scbond_it 3.036 r_scbond_other 3.032
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.529 r_dihedral_angle_3_deg 11.864 r_dihedral_angle_1_deg 5.319 r_lrange_it 4.558 r_lrange_other 4.519 r_dihedral_angle_2_deg 4.206 r_scangle_it 4.021 r_scangle_other 4.017 r_scbond_it 3.036 r_scbond_other 3.032 r_mcangle_it 2.54 r_mcangle_other 2.54 r_mcbond_it 2.06 r_mcbond_other 2.059 r_angle_refined_deg 1.553 r_angle_other_deg 0.766 r_dihedral_angle_other_2_deg 0.575 r_nbd_refined 0.219 r_symmetry_xyhbond_nbd_refined 0.208 r_symmetry_nbd_other 0.207 r_nbd_other 0.198 r_symmetry_nbd_refined 0.188 r_nbtor_refined 0.182 r_xyhbond_nbd_refined 0.107 r_chiral_restr 0.077 r_symmetry_nbtor_other 0.077 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 r_gen_planes_other 0.004 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4977 Nucleic Acid Atoms Solvent Atoms 437 Heterogen Atoms 125
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing