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Crystal Structure of Diacylglycerol Kinase DgkB in complex with ADP and Mg
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 8.5 277 drop: 0.1 M Tris pH 8.5, 9% PEG2K MME;
well: 0.1 M Tris pH 8.5, 18% PEG2K MME, VAPOR DIFFUSION, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.41 48.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 123.76 α = 90 b = 123.76 β = 90 c = 47.68 γ = 90
Symmetry Space Group P 42 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 170 CCD MARMOSAIC 300 mm CCD mirrors 2007-03-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.0 APS 22-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 2.3 30 99.8 0.128 24.5 12.2 17025 16997
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 2.3 2.38 99.8 0.431 4.2 8.3 1667
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (All) 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 Rigid body refinement of DgkB THROUGHOUT 2.3 29.17 16997 16069 857 99.58 0.20845 0.20648 0.2057 0.2464 0.246 RANDOM 34.138
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] -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.929 r_dihedral_angle_4_deg 17.523 r_dihedral_angle_3_deg 14.053 r_dihedral_angle_1_deg 5.887 r_scangle_it 1.603 r_angle_refined_deg 1.122 r_scbond_it 1.093 r_mcangle_it 0.676 r_mcbond_it 0.43 r_nbtor_refined 0.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.929 r_dihedral_angle_4_deg 17.523 r_dihedral_angle_3_deg 14.053 r_dihedral_angle_1_deg 5.887 r_scangle_it 1.603 r_angle_refined_deg 1.122 r_scbond_it 1.093 r_mcangle_it 0.676 r_mcbond_it 0.43 r_nbtor_refined 0.3 r_symmetry_hbond_refined 0.189 r_nbd_refined 0.177 r_symmetry_vdw_refined 0.171 r_xyhbond_nbd_refined 0.107 r_chiral_restr 0.061 r_bond_refined_d 0.007 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2324 Nucleic Acid Atoms Solvent Atoms 152 Heterogen Atoms 28
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling DgkB phasing