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Glutamate 5-kinase from Escherichia coli complexed with glutamate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2J5V PARTIALLY-REFINED MODEL OF PBD ENTRY 2J5V
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.5 1.45 M MGSO4, 20 MM CACL2, 0.1 M MES PH 6.5.
Crystal Properties Matthews coefficient Solvent content 2.77 55.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.302 α = 90 b = 124.108 β = 93.96 c = 144.927 γ = 90
Symmetry Space Group P 1 21 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 CCD TOROIDAL MIRRORS 2005-02-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 ESRF ID14-4
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 2.9 50 99.3 0.16 9.7 4.5 74908 2.9
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 2.9 3.06 99.6 0.49 2.9 4.6
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 PARTIALLY-REFINED MODEL OF PBD ENTRY 2J5V 2.9 25 70989 3771 99.2 0.199 0.197 0.208 0.246 0.2513 RANDOM 24.57
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] -2.13 0.38 3.82 -1.63
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.96 r_dihedral_angle_3_deg 17.532 r_dihedral_angle_4_deg 15.682 r_dihedral_angle_1_deg 5.796 r_scangle_it 1.281 r_angle_refined_deg 1.159 r_scbond_it 0.774 r_angle_other_deg 0.745 r_mcangle_it 0.538 r_mcbond_it 0.52
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.96 r_dihedral_angle_3_deg 17.532 r_dihedral_angle_4_deg 15.682 r_dihedral_angle_1_deg 5.796 r_scangle_it 1.281 r_angle_refined_deg 1.159 r_scbond_it 0.774 r_angle_other_deg 0.745 r_mcangle_it 0.538 r_mcbond_it 0.52 r_symmetry_vdw_refined 0.261 r_symmetry_hbond_refined 0.214 r_nbd_refined 0.198 r_symmetry_vdw_other 0.185 r_nbd_other 0.176 r_nbtor_refined 0.164 r_xyhbond_nbd_refined 0.135 r_nbtor_other 0.083 r_chiral_restr 0.061 r_bond_refined_d 0.009 r_gen_planes_refined 0.003 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_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 21321 Nucleic Acid Atoms Solvent Atoms 103 Heterogen Atoms 188
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling MOLREP phasing