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Crystal Structure of a Semialdehyde dehydrogenase NAD-binding Protein from Cupriavidus necator in Complex with Calcium and NAD
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3C24
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.2 M CaCl2, 20 (w/v) PEB-3350, 5 mM Mg, 5 mM NAD+
Crystal Properties Matthews coefficient Solvent content 2.46 49.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.903 α = 90 b = 71.14 β = 90 c = 47.649 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 100 CCD ADSC QUANTUM 315 Diamond 2016-06-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 31-ID 0.97931 APS 31-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.646 19.956 99.9 0.114 8.7 6.9 36952
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 1.65 1.73 100 0.919 0.8 6.9
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 3C24 1.65 19.956 35109 1792 99.82 0.1742 0.1727 0.1839 0.2031 0.2086 RANDOM 24.885
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] -1.13 0.47 0.66
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.961 r_dihedral_angle_4_deg 15.084 r_dihedral_angle_3_deg 13.666 r_dihedral_angle_1_deg 5.712 r_mcangle_it 3.15 r_mcbond_it 2.249 r_mcbond_other 2.241 r_angle_refined_deg 1.956 r_angle_other_deg 1.096 r_chiral_restr 0.131
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.961 r_dihedral_angle_4_deg 15.084 r_dihedral_angle_3_deg 13.666 r_dihedral_angle_1_deg 5.712 r_mcangle_it 3.15 r_mcbond_it 2.249 r_mcbond_other 2.241 r_angle_refined_deg 1.956 r_angle_other_deg 1.096 r_chiral_restr 0.131 r_bond_refined_d 0.021 r_gen_planes_refined 0.01 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2123 Nucleic Acid Atoms Solvent Atoms 134 Heterogen Atoms 46
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction MOSFLM data reduction SCALA data scaling PHASER phasing