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Structure of the yeast coat nucleoporin complex, space group C2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3IKO 3IKO, 3F3F, 3F7F, and 3PGF experimental model PDB 3F3F 3IKO, 3F3F, 3F7F, and 3PGF experimental model PDB 3F7F 3IKO, 3F3F, 3F7F, and 3PGF experimental model PDB 3PGF 3IKO, 3F3F, 3F7F, and 3PGF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 294 PEG 20000, ethanol, MES
Crystal Properties Matthews coefficient Solvent content 4.23 70.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 210.645 α = 90 b = 186.297 β = 100.85 c = 199.57 γ = 90
Symmetry Space Group C 1 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 2014-08-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 0.9794 APS 23-ID-D
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 7.384 70 99 0.097 15.3 13.5 10375
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 7.384 7.8 94.9 0.212 1.4 13.5
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3IKO, 3F3F, 3F7F, and 3PGF 7.384 67.516 1.33 10227 1022 99.47 0.3322 0.3299 0.335 0.3527 0.3583 Random selection
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 15.761 f_angle_d 1.217 f_chiral_restr 0.051 f_plane_restr 0.007 f_bond_d 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 26139 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling PHASER phasing