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Crystal structure of human diacylglycerol kinase alpha EF-hand domains bound to Ca2+
Serial Crystallography (SX)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 296 0.1 M HEPES, 1.0 M succinic acid, 2 % PEG monomethyl ether 2000, 10 % glycerol
Crystal Properties Matthews coefficient Solvent content 2.82 56.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.19 α = 90 b = 58.19 β = 90 c = 61.12 γ = 120
Symmetry Space Group P 32 2 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 PIXEL DECTRIS EIGER X 4M 2017-11-27 M SINGLE WAVELENGTH 2 1 100 PIXEL DECTRIS EIGER X 4M 2018-03-06
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-1A 1.1 Photon Factory BL-1A
Serial Crystallography Sample delivery method Diffraction ID Description Sample Delivery Method 2 fixed target
Fixed Target Diffraction ID Description Sample Holding Support Base Motion control Details Sample Solvent 2 cryo loop goniometer
Data Reduction Diffraction ID Frames Indexed Crystal Hits Frames Indexed Latices Merged 2 14400 14400
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Rpim I (All) CC (Half) 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 2.142 50 99.9 0.083 0.083 0.028 0.998 15.13 9.7 6876 44.49
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.142 2.27 99.2 0.661 0.698 0.881 2.91 9.88
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION SAD THROUGHOUT 2.142 38.882 1.39 6875 344 99.85 0.1879 0.1854 0.1888 0.2376 0.249 60.056
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 8.402 f_angle_d 1.315 f_chiral_restr 0.069 f_bond_d 0.013 f_plane_restr 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 694 Nucleic Acid Atoms Solvent Atoms 9 Heterogen Atoms 40
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PDB_EXTRACT data extraction AutoSol phasing Coot model building PHENIX model building