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Crystal structure of the SERCA2a in the E2.ATP state
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3AR4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.2 283 5% glycerol, 20-23% PEG1500, 5 mM MgSO4, 6 mM EGTA, 6% 2-methyl-2,4-pentanediol (MPD) and 100 mM MOPS pH 7.2
Crystal Properties Matthews coefficient Solvent content 3.64 66.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 121.604 α = 90 b = 270.382 β = 90 c = 97.34 γ = 90
Symmetry Space Group C 2 2 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 40 PIXEL DECTRIS PILATUS3 6M 2016-04-10 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) Rrim 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 2.6 30 97.9 0.097 0.103 0.995 19.6 9.4 48563 65.0535037813
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 2.6 2.68 88.2 0.856 0.98 0.577 1.3 3.6
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 3AR4 3.00002849524 14.9879317255 2.00125865324 31360 1568 97.1288753988 0.193939305416 0.192444544089 0.1923 0.222002563214 0.2166 117
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 12.4099805954 f_angle_d 1.10742163013 f_chiral_restr 0.302679907466 f_bond_d 0.00648257671243 f_plane_restr 0.00582423078848
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7639 Nucleic Acid Atoms Solvent Atoms 102 Heterogen Atoms 128
Software Software Software Name Purpose DENZO data reduction PHENIX refinement SCALEPACK data scaling CNS phasing CNS refinement