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Crystal structure of alpha-ketoglutarate semialdehyde dehydrogenase (KGSADH) from Azospirillum brasilense
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2W8R
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 277 16% polyethylene glycol 3350, 0.1 M sodium cacodylate pH 6.5, and 0.2 M Magnesium chloride hexahydrate
Crystal Properties Matthews coefficient Solvent content 2.44 49.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 129.04 α = 90 b = 129.04 β = 90 c = 118.093 γ = 90
Symmetry Space Group P 43 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 100 CCD ADSC QUANTUM 270 2015-11-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 7A (6B, 6C1) 0.97934 PAL/PLS 7A (6B, 6C1)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.25 129.1 95.1 27.63 3.4 43134
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.25 2.29
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 2W8R 2.25 30.606 43134 2268 95.02 0.1777 0.1744 0.1815 0.24 0.2423 RANDOM 30.362
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] -0.54 -0.54 1.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.49 r_dihedral_angle_4_deg 18.641 r_dihedral_angle_3_deg 15.14 r_dihedral_angle_1_deg 6.701 r_angle_refined_deg 1.774 r_angle_other_deg 1.037 r_chiral_restr 0.102 r_bond_refined_d 0.016 r_gen_planes_refined 0.009 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.49 r_dihedral_angle_4_deg 18.641 r_dihedral_angle_3_deg 15.14 r_dihedral_angle_1_deg 6.701 r_angle_refined_deg 1.774 r_angle_other_deg 1.037 r_chiral_restr 0.102 r_bond_refined_d 0.016 r_gen_planes_refined 0.009 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7096 Nucleic Acid Atoms Solvent Atoms 426 Heterogen Atoms 6
Software Software Software Name Purpose HKL-2000 data collection REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction HKL-2000 data scaling HKL-2000 phasing HKL data reduction