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Crystal structure of Vesicle-associated membrane protein-associated protein SCS2 from yeast
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 289.15 25% PEG 3350, 0.1 mM tris-bis (pH 5.5). 0.1 M EDTA
Crystal Properties Matthews coefficient Solvent content 2.76 55.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.689 α = 90 b = 68.689 β = 90 c = 56.374 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 PILATUS 6M 2020-05-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL19U1 0.978520 SSRF BL19U1
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 2 50 99.81 0.05229 0.01233 1 37.12 19 10680 39.82
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.09 0.6431 0.1588 0.95 4.49
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 MOLECULAR REPLACEMENT FREE R-VALUE 2 40.92 1.35 10680 1058 99.81 0.2505 0.2495 0.2495 0.2606 0.2608 45.45
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 17.8156 f_angle_d 0.6275 f_chiral_restr 0.0473 f_bond_d 0.0034 f_plane_restr 0.0034
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 980 Nucleic Acid Atoms Solvent Atoms 47 Heterogen Atoms 20
Software Software Software Name Purpose PHENIX refinement Coot model building iMOSFLM data reduction Aimless data scaling PHASER phasing