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Crystal Structure of Threonine-sensitive Aspartokinase from Methanococcus jannaschii with L-aspartate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3C1M PDB code:3C1M
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 293 14% PEG4000, 0.1M Tris, 0.8M ammonium formate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.52 51.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 107.973 α = 90 b = 199.071 β = 90 c = 96.394 γ = 90
Symmetry Space Group C 2 2 21
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 MARMOSAIC 300 mm CCD 2006-12-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 17-ID 1.039 APS 17-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 2.7 50 0.91 0.076 28.3 3.7 30974 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) 1 2.7 2.77 0.395 3 3.4
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 THROUGHOUT PDB code:3C1M 2.7 50 27389 1466 99.75 0.23976 0.23794 0.2256 0.27298 0.2613 RANDOM 33.893
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] 1.35 -1.95 0.61
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.122 r_dihedral_angle_3_deg 18.517 r_dihedral_angle_4_deg 12.411 r_dihedral_angle_1_deg 5.711 r_scangle_it 1.428 r_angle_refined_deg 1.183 r_scbond_it 0.798 r_mcangle_it 0.653 r_mcbond_it 0.371 r_nbtor_refined 0.305
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.122 r_dihedral_angle_3_deg 18.517 r_dihedral_angle_4_deg 12.411 r_dihedral_angle_1_deg 5.711 r_scangle_it 1.428 r_angle_refined_deg 1.183 r_scbond_it 0.798 r_mcangle_it 0.653 r_mcbond_it 0.371 r_nbtor_refined 0.305 r_nbd_refined 0.217 r_symmetry_vdw_refined 0.202 r_symmetry_hbond_refined 0.152 r_xyhbond_nbd_refined 0.131 r_chiral_restr 0.11 r_bond_refined_d 0.009 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7075 Nucleic Acid Atoms Solvent Atoms 13 Heterogen Atoms 24
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction CrystalClear data collection CrystalClear data reduction CrystalClear data scaling PHASER phasing