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Crystal structure of aspartate aminotransferase (AspAT) from Corynebacterium glutamicum ATCC 13032
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3D6K
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 PEG 3350, Ammonium citrate
Crystal Properties Matthews coefficient Solvent content 2.46 50.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 103.388 α = 90 b = 53.521 β = 104.23 c = 170.224 γ = 90
Symmetry Space Group C 1 2 1
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 2014-12-23 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 1.999 165 97.7 41.61 3.6 56893
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 2.03
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 3D6K 2 165 56893 3050 97.44 0.1509 0.1484 0.1617 0.1986 0.2086 RANDOM 14.498
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] -0.19 -0.89 1.28 -0.57
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.289 r_dihedral_angle_4_deg 13.717 r_dihedral_angle_3_deg 12.364 r_dihedral_angle_1_deg 6.458 r_angle_refined_deg 1.888 r_mcangle_it 1.824 r_mcbond_it 1.21 r_mcbond_other 1.208 r_angle_other_deg 1.061 r_chiral_restr 0.115
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.289 r_dihedral_angle_4_deg 13.717 r_dihedral_angle_3_deg 12.364 r_dihedral_angle_1_deg 6.458 r_angle_refined_deg 1.888 r_mcangle_it 1.824 r_mcbond_it 1.21 r_mcbond_other 1.208 r_angle_other_deg 1.061 r_chiral_restr 0.115 r_bond_refined_d 0.019 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 6540 Nucleic Acid Atoms Solvent Atoms 756 Heterogen Atoms 105
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection PDB_EXTRACT data extraction HKL-2000 data reduction HKL-2000 data scaling HKL-2000 phasing