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Crystal structure of yeast Sec62 cytoplasmic domain
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 277 100mM MES pH 5.7-5.9, 2 M (NH4)2SO4
Crystal Properties Matthews coefficient Solvent content 3.64 66.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 99.206 α = 90 b = 99.206 β = 90 c = 155.657 γ = 120
Symmetry Space Group P 65 2 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 2017-05-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM02 0.97958 ESRF BM02
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 2.54 47.26 99.81 0.1075 0.109 0.01778 1 26.56 38.1 15563 74.11
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 2.54 2.63 1.869 1.894 0.949 2.03
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 FREE R-VALUE 2.54 47.26 1.38 15563 778 99.68 0.2225 0.2206 0.2289 0.2598 0.268 75.34
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 23.5407 f_angle_d 1.729 f_chiral_restr 0.0631 f_bond_d 0.0128 f_plane_restr 0.0094
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2108 Nucleic Acid Atoms Solvent Atoms 76 Heterogen Atoms 99
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling PHENIX phasing