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The crystal structure of L-Sorbose reductase from Gluconobacter frateurii complexed with NADPH and L-sorbose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3AI2 PDB ENTRY 3AI2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.5 293 Crystals of the His116Leu mutant of SR containing 10 mM NADPH and 100 mM L-sorbose were obtained under a reservoir solution condition of 30% (w/v) PEG400, 200 mM calcium chloride and 100 mM sodium acetate trihydrate, pH 4.5. The crystals of SR complexed with NADPH and L-sorbose were prepared by soaking the crystals in the reservoir solution supplemented with 2 M L-sorbose and 10 mM NADPH for 12 h at 293 K., VAPOR DIFFUSION, SITTING DROP, temperature 293.0K
Crystal Properties Matthews coefficient Solvent content 2.09 41.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.04 α = 90 b = 124.41 β = 90 c = 124.54 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 CCD ADSC QUANTUM 270 2009-10-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NE3A 1.000 Photon Factory AR-NE3A
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 20 99.8 0.083 21.3 88419 1.0001 1
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 1.8 1.85 100 0.465 5.6
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 PDB ENTRY 3AI2 1.8 19.69 83987 4432 99.84 0.21416 0.2123 0.1742 0.24941 0.2038 RANDOM 12.871
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] 0.93 0.51 -1.44
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.165 r_dihedral_angle_4_deg 15.829 r_dihedral_angle_3_deg 13.697 r_dihedral_angle_1_deg 5.584 r_scangle_it 3.831 r_scbond_it 2.358 r_angle_refined_deg 1.476 r_mcangle_it 1.308 r_mcbond_it 0.693 r_chiral_restr 0.099
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.165 r_dihedral_angle_4_deg 15.829 r_dihedral_angle_3_deg 13.697 r_dihedral_angle_1_deg 5.584 r_scangle_it 3.831 r_scbond_it 2.358 r_angle_refined_deg 1.476 r_mcangle_it 1.308 r_mcbond_it 0.693 r_chiral_restr 0.099 r_bond_refined_d 0.013 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7956 Nucleic Acid Atoms Solvent Atoms 368 Heterogen Atoms 300
Software Software Software Name Purpose ADSC data collection REFMAC refinement XDS data reduction XDS data scaling