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Crystal structure of aspartate kinase from Corynebacterium glutamicum in complex with threonine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3AAW PDB ENTRY 3AAW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 2.2M Ammonium sulfate, 0.05M HEPES-NaOH, 2.1% PEG 400, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.55 51.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 101.833 α = 71.85 b = 119.093 β = 69.48 c = 124.384 γ = 72.72
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 315r mirrors 2008-12-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1 Photon Factory BL-5A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.59 50 98.2 0.15 0.15 6.7 3.8 156726 79.2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.59 2.69 96.4 0.47 0.84 3.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 PDB ENTRY 3AAW 2.59 42.04 153824 146136 7700 97.13 0.2344 0.23198 0.2265 0.28025 0.2737 RANDOM 62.201
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] 0.01 -0.01 -0.01 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.158 r_dihedral_angle_3_deg 15.786 r_dihedral_angle_4_deg 15.399 r_dihedral_angle_1_deg 5.344 r_angle_refined_deg 0.905 r_scangle_it 0.894 r_angle_other_deg 0.787 r_scbond_it 0.498 r_mcangle_it 0.437 r_mcbond_it 0.234
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.158 r_dihedral_angle_3_deg 15.786 r_dihedral_angle_4_deg 15.399 r_dihedral_angle_1_deg 5.344 r_angle_refined_deg 0.905 r_scangle_it 0.894 r_angle_other_deg 0.787 r_scbond_it 0.498 r_mcangle_it 0.437 r_mcbond_it 0.234 r_chiral_restr 0.051 r_mcbond_other 0.024 r_bond_refined_d 0.006 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 31609 Nucleic Acid Atoms Solvent Atoms 246 Heterogen Atoms 120
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling