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Crystal structure of SR Ca2+-ATPase in E2(TG) with bound MPQ
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2AGV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICRODIALYSIS 6.1 283 25% glycerol, 4% polyethylene glycol 400, 20 mM 2-(N-morpholino)ethanesulfonic acid-NaOH, 5 mM sodium azide, 0.2 mM dithiothreitol, 2ug/ml butylhydroxytoluene, 3 mM EGTA
Crystal Properties Matthews coefficient Solvent content 3.41 63.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.479 α = 90 b = 71.479 β = 90 c = 590.593 γ = 90
Symmetry Space Group P 41 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 100 PIXEL DECTRIS EIGER X 16M 2017-11-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 1 SPring-8 BL41XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.2 50 99.8 0.994 12.9 15.5 79896 40.82
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 2.2 2.24 96.4 0.695 2.9 13.6
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 2AGV 2.2 14.99 1.36 79564 2000 99.82 0.2209 0.2198 0.2245 0.2613 0.2632 52.3
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 15.9637 f_angle_d 1.2568 f_chiral_restr 0.3528 f_plane_restr 0.0105 f_bond_d 0.0073
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7671 Nucleic Acid Atoms Solvent Atoms 328 Heterogen Atoms 224
Software Software Software Name Purpose PHENIX refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing