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Crystal structure of inositol dehydrogenase homolog complexed with NAD+ from Azotobacter vinelandii
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3DTY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 0.1 M ammonium tartrate dibasic, pH 7.0, 12% (w/v) PEG 3350, 10 mM NAD+
Crystal Properties Matthews coefficient Solvent content 2.6 52.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.25 α = 90 b = 107.997 β = 90 c = 156.759 γ = 90
Symmetry Space Group I 2 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 95 CCD ADSC QUANTUM 210 2011-06-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 0.9800 Photon Factory BL-5A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.75 50 99.7 0.041 0.997 33.1 3.6 46835
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.75 1.78 0.208 0.95 6 2.7
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 3DTY 1.75 37.663 46817 2274 99.541 0.18 0.1789 0.1893 0.1933 0.1991 15.538
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] 1.523 -0.83 -0.692
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.432 r_dihedral_angle_4_deg 17.127 r_dihedral_angle_3_deg 12.502 r_dihedral_angle_1_deg 7.026 r_lrange_it 3.103 r_lrange_other 3.03 r_scangle_it 2.119 r_scangle_other 2.118 r_angle_other_deg 1.383 r_scbond_it 1.366
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.432 r_dihedral_angle_4_deg 17.127 r_dihedral_angle_3_deg 12.502 r_dihedral_angle_1_deg 7.026 r_lrange_it 3.103 r_lrange_other 3.03 r_scangle_it 2.119 r_scangle_other 2.118 r_angle_other_deg 1.383 r_scbond_it 1.366 r_scbond_other 1.366 r_mcangle_it 1.338 r_angle_refined_deg 1.337 r_mcangle_other 1.337 r_mcbond_it 0.82 r_mcbond_other 0.82 r_symmetry_nbd_refined 0.244 r_nbd_other 0.208 r_nbd_refined 0.197 r_symmetry_nbd_other 0.186 r_nbtor_refined 0.161 r_xyhbond_nbd_refined 0.12 r_symmetry_xyhbond_nbd_refined 0.085 r_symmetry_nbtor_other 0.076 r_chiral_restr 0.07 r_bond_refined_d 0.006 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3027 Nucleic Acid Atoms Solvent Atoms 273 Heterogen Atoms 44
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing