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Crystal Structure of Diacylglycerol Kinase
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 277 drop: 0.1 M Tris pH 8.5, 9% PEG2KMME;
well: 0.1 M Tris pH 8.5, 18% PEG2KMME, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.47 50.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 124.21 α = 90 b = 124.21 β = 90 c = 48.502 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 2007-02-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 0.9794 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 2.4 26.15 99.8 0.094 28.1 8.8 15527 15472
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) 2.4 2.49 99.5 0.376 8.2 6.1 1491
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 SAD THROUGHOUT 2.4 26.15 15601 14042 730 94.69 0.23087 0.22869 0.2278 0.27213 0.2737 RANDOM 39.969
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 -0.01 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.432 r_dihedral_angle_3_deg 18.402 r_dihedral_angle_4_deg 16.672 r_dihedral_angle_1_deg 6.828 r_scangle_it 3.44 r_scbond_it 2.269 r_mcangle_it 1.336 r_angle_refined_deg 1.335 r_mcbond_it 1.111 r_nbtor_refined 0.303
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.432 r_dihedral_angle_3_deg 18.402 r_dihedral_angle_4_deg 16.672 r_dihedral_angle_1_deg 6.828 r_scangle_it 3.44 r_scbond_it 2.269 r_mcangle_it 1.336 r_angle_refined_deg 1.335 r_mcbond_it 1.111 r_nbtor_refined 0.303 r_symmetry_vdw_refined 0.247 r_nbd_refined 0.203 r_xyhbond_nbd_refined 0.172 r_symmetry_hbond_refined 0.161 r_chiral_restr 0.086 r_bond_refined_d 0.01 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2171 Nucleic Acid Atoms Solvent Atoms 116 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling SOLVE phasing