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Unique GTP-binding Pocket and Allostery of UMP Kinase from a Gram-Negative Phytopathogen Bacterium
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3EK6 PDB ENTRY 3EK6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 298 0.1M Na Citrate, 19.5% PEG 3350, 0.05M (NH4)2SO4, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.67 53.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 111.634 α = 90 b = 119.638 β = 90 c = 125.18 γ = 90
Symmetry Space Group P 21 21 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 ADSC QUANTUM 210 2007-12-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE BL13C1 0.97315 NSRRC BL13C1
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 2.56 86.39 99.7 0.063 0.05 23.7 5.4 55638 55392 2 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.56 2.65 99.8 0.504 0.3 3.3 5
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 3EK6 2.56 27.3 52509 2814 98.95 0.20858 0.20626 0.25157 0.2595 RANDOM 55.136
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] 1.46 1.2 -2.66
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.421 r_dihedral_angle_4_deg 18.391 r_dihedral_angle_3_deg 17.823 r_dihedral_angle_1_deg 4.843 r_scangle_it 1.766 r_mcangle_it 1.755 r_angle_refined_deg 1.382 r_mcbond_it 1.041 r_scbond_it 1.025 r_symmetry_vdw_refined 0.361
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.421 r_dihedral_angle_4_deg 18.391 r_dihedral_angle_3_deg 17.823 r_dihedral_angle_1_deg 4.843 r_scangle_it 1.766 r_mcangle_it 1.755 r_angle_refined_deg 1.382 r_mcbond_it 1.041 r_scbond_it 1.025 r_symmetry_vdw_refined 0.361 r_nbtor_refined 0.33 r_nbd_refined 0.268 r_symmetry_hbond_refined 0.265 r_xyhbond_nbd_refined 0.219 r_chiral_restr 0.083 r_bond_refined_d 0.012 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 10785 Nucleic Acid Atoms Solvent Atoms 507 Heterogen Atoms 192
Software Software Software Name Purpose HKL-2000 data collection SOLVE phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling