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Crystal structure of ATP11C-CDC50A in PtdSer-bound E2P state
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6K7L
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293.15 14-15% PEG4000, 10% glycerol, 5 mM beta-mercaptoethanol, 0.4 M MgSO4
Crystal Properties Matthews coefficient Solvent content 4.23 70.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 100.46 α = 90 b = 232.83 β = 90 c = 492.89 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 80 PIXEL DECTRIS EIGER X 16M 2019-04-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 1.0 SPring-8 BL41XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 3.9 50 71.32 1.141 0.0419 0.92 15.88 776.9 106458 98.24
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.9 4 11.64 0.864 698.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 MOLECULAR REPLACEMENT FREE R-VALUE 6k7l 3.9 49.97 2.07 75980 3779 71.37 0.2846 0.2812 0.283 0.3501 0.3502 161.97
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 20.5195 f_angle_d 1.1933 f_chiral_restr 0.0925 f_plane_restr 0.0082 f_bond_d 0.0062
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 44860 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 396
Software Software Software Name Purpose PHENIX refinement PHENIX model building XDS data reduction XDS data scaling PHASER phasing