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Structure of sorbitol dehydrogenase from Sinorhizobium meliloti 1021 bound to sorbitol
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6PEI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 50 mM sodium acetate, 100 mM HEPES pH 7.4, 18% PEG 3000, 20% sorbitol
Crystal Properties Matthews coefficient Solvent content 2.31 46.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.298 α = 90 b = 88.298 β = 117.39 c = 87.317 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 93 IMAGE PLATE RIGAKU RAXIS IV++ 2017-04-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5419
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 2 39.6 98 0.139 5.4 3 74395
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 2 10 0.522
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 6PEI 2 39.08 70800 3581 97.92 0.1968 0.1941 0.2494 0.27 RANDOM 19.442
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] 0.99 -1.58 -0.01 0.43
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.743 r_dihedral_angle_4_deg 19.488 r_dihedral_angle_3_deg 16.796 r_dihedral_angle_1_deg 7.256 r_mcangle_it 2.581 r_angle_other_deg 2.469 r_angle_refined_deg 1.927 r_mcbond_it 1.848 r_mcbond_other 1.848 r_chiral_restr 0.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.743 r_dihedral_angle_4_deg 19.488 r_dihedral_angle_3_deg 16.796 r_dihedral_angle_1_deg 7.256 r_mcangle_it 2.581 r_angle_other_deg 2.469 r_angle_refined_deg 1.927 r_mcbond_it 1.848 r_mcbond_other 1.848 r_chiral_restr 0.1 r_bond_other_d 0.037 r_bond_refined_d 0.015 r_gen_planes_other 0.015 r_gen_planes_refined 0.011
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7588 Nucleic Acid Atoms Solvent Atoms 905 Heterogen Atoms 48
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction XDS data scaling PHASER phasing