☰ Navigation Tabs
Crystal structure of inositol dehydrogenase homolog complexed with NADH and myo-inositol 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 293 0.2 M Ca acetate, 14% PEG3350,10 mM NADH, 50 mM myo-inositol
Crystal Properties Matthews coefficient Solvent content 2.04 39.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 99.81 α = 90 b = 151.53 β = 90 c = 48.12 γ = 90
Symmetry Space Group P 21 21 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 315 2011-11-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-17A 0.980 Photon Factory BL-17A
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 1.8 50 92.5 0.064 0.999 19.9 6.9 63455
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 1.8 1.85 59.7 0.558 0.788 2.5 5.3
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 1.8 48.166 63455 3177 92.482 0.18 0.1794 0.1874 0.1969 0.2005 22.52
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] 0.458 -0.964 0.506
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.58 r_dihedral_angle_4_deg 20.047 r_dihedral_angle_3_deg 12.244 r_dihedral_angle_1_deg 6.897 r_lrange_it 4.326 r_lrange_other 4.324 r_scangle_it 3.452 r_scangle_other 3.451 r_mcangle_it 2.145 r_mcangle_other 2.145
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.58 r_dihedral_angle_4_deg 20.047 r_dihedral_angle_3_deg 12.244 r_dihedral_angle_1_deg 6.897 r_lrange_it 4.326 r_lrange_other 4.324 r_scangle_it 3.452 r_scangle_other 3.451 r_mcangle_it 2.145 r_mcangle_other 2.145 r_scbond_it 2.144 r_scbond_other 2.144 r_angle_other_deg 1.499 r_mcbond_it 1.438 r_mcbond_other 1.435 r_angle_refined_deg 1.425 r_symmetry_nbd_refined 0.278 r_nbd_other 0.248 r_nbd_refined 0.201 r_symmetry_nbd_other 0.196 r_nbtor_refined 0.165 r_xyhbond_nbd_refined 0.129 r_symmetry_xyhbond_nbd_refined 0.093 r_symmetry_nbtor_other 0.082 r_chiral_restr 0.076 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5972 Nucleic Acid Atoms Solvent Atoms 273 Heterogen Atoms 100
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing