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Crystal structure of the aminoacid kinase domain of the glutamate 5 kinase of Escherichia coli.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2J5T PDB ENTRY 2J5T
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5.6 LITHIUM SULFATE 1M, AMMONIUM SULFATE 0.5M, SODIUM SITRATE 0.1M PH 5.6
Crystal Properties Matthews coefficient Solvent content 4.15 70.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 141.358 α = 90 b = 141.358 β = 90 c = 78.373 γ = 120
Symmetry Space Group P 62 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 315r MIRRORS 2008-06-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM30A ESRF BM30A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.95 122.17 100 0.11 5.6 15.4 10173 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.95 3.11 100 0.44 1.7 15.7
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 PDB ENTRY 2J5T 2.95 50 9677 490 100 0.209 0.206 0.2034 0.259 0.2366 RANDOM 52.6
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] -1.95 -0.97 -1.95 2.92
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.08 r_dihedral_angle_4_deg 23.117 r_dihedral_angle_3_deg 21.437 r_dihedral_angle_1_deg 8.401 r_scangle_it 3.873 r_scbond_it 2.232 r_angle_refined_deg 1.901 r_mcangle_it 1.704 r_mcbond_it 0.915 r_symmetry_hbond_refined 0.491
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.08 r_dihedral_angle_4_deg 23.117 r_dihedral_angle_3_deg 21.437 r_dihedral_angle_1_deg 8.401 r_scangle_it 3.873 r_scbond_it 2.232 r_angle_refined_deg 1.901 r_mcangle_it 1.704 r_mcbond_it 0.915 r_symmetry_hbond_refined 0.491 r_nbtor_refined 0.314 r_nbd_refined 0.251 r_symmetry_vdw_refined 0.247 r_xyhbond_nbd_refined 0.146 r_chiral_restr 0.134 r_bond_refined_d 0.018 r_gen_planes_refined 0.005 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_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1788 Nucleic Acid Atoms Solvent Atoms 4 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling MOLREP phasing