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Crystal structure of aspartate kinase from Corynebacterium glutamicum in complex with lysine and threonine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2HMF PDB ENTRIES 2HMF and 2DTJ experimental model PDB 2DTJ PDB ENTRIES 2HMF and 2DTJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 293 1.2M Sodium citrate, 0.1M Tris-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.41 63.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 162.232 α = 90 b = 162.232 β = 90 c = 133.926 γ = 90
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 4r mirror 2007-10-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-6A 0.978 Photon Factory BL-6A
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 2.5 50 99.8 0.056 0.056 27.1 7.6 59981 59.2
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) 2.5 2.59 100 0.338 5.8 7.7
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 (All) 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 ENTRIES 2HMF and 2DTJ 2.5 43.56 59980 56782 3022 99.71 0.21188 0.21188 0.20985 0.2081 0.25029 0.2453 RANDOM 45.963
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] -1.36 -1.36 2.72
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.572 r_dihedral_angle_4_deg 17.084 r_dihedral_angle_3_deg 15.716 r_dihedral_angle_1_deg 5.429 r_scangle_it 2.122 r_scbond_it 1.2 r_angle_refined_deg 1.066 r_mcangle_it 0.94 r_angle_other_deg 0.838 r_mcbond_it 0.493
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.572 r_dihedral_angle_4_deg 17.084 r_dihedral_angle_3_deg 15.716 r_dihedral_angle_1_deg 5.429 r_scangle_it 2.122 r_scbond_it 1.2 r_angle_refined_deg 1.066 r_mcangle_it 0.94 r_angle_other_deg 0.838 r_mcbond_it 0.493 r_chiral_restr 0.063 r_mcbond_other 0.058 r_bond_refined_d 0.008 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8199 Nucleic Acid Atoms Solvent Atoms 222 Heterogen Atoms 62
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling