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The crystal structure of L-sorbose reductase from Gluconobacter frateurii complexed with NADPH
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3AI1 PDB ENTRY 3AI1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.5 293 5MM NADPH, 34% (W/V) PEG 400, 200MM CALCIUM ACETATE, 100MM SODIUM ACETATE TRIHYDRATE PH 4.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K, temperature 293.0K
Crystal Properties Matthews coefficient Solvent content 2.08 40.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 124.29 α = 90 b = 60.98 β = 89.99 c = 124.45 γ = 90
Symmetry Space Group P 1 21 1
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 315 2008-06-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.000 Photon Factory BL-5A
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 1.9 50 99.7 0.07 11.1 146936 1 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 1.9 1.95 99.8 0.383 3.4
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 3AI1 1.9 19.67 139564 7364 99.8 0.175 0.172 0.1732 0.221 0.221 RANDOM 19.4
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.995 r_dihedral_angle_4_deg 18.842 r_dihedral_angle_3_deg 14.412 r_dihedral_angle_1_deg 5.918 r_scangle_it 4.711 r_scbond_it 2.907 r_angle_refined_deg 1.746 r_mcangle_it 1.653 r_mcbond_it 0.964 r_chiral_restr 0.116
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.995 r_dihedral_angle_4_deg 18.842 r_dihedral_angle_3_deg 14.412 r_dihedral_angle_1_deg 5.918 r_scangle_it 4.711 r_scbond_it 2.907 r_angle_refined_deg 1.746 r_mcangle_it 1.653 r_mcbond_it 0.964 r_chiral_restr 0.116 r_bond_refined_d 0.02 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 15928 Nucleic Acid Atoms Solvent Atoms 1411 Heterogen Atoms 384
Software Software Software Name Purpose ADSC data collection MOLREP phasing REFMAC refinement XDS data reduction XDS data scaling