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High resolution crystal structure of C-terminal domain (residues 715-866) of Nucleoporin-98
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5E0Q
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 278 8% (v/w) PEG 6000, 8% (v/v) 2-methy-2,4-pentanediol, 0.1 M HEPES
Crystal Properties Matthews coefficient Solvent content 3.45 66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.07 α = 90 b = 72.07 β = 90 c = 91.82 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 PILATUS 6M Dynamically bendable mirrow 2018-10-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 1.000 SLS X10SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.5 44.6 100 0.148 0.015 1 33.4 90.2 39371 20.85
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.5 1.54 100 0.47 1.1 0.42 0.8 37.8
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 5E0Q 1.5 44.56 1.35 39370 1969 99.98 0.1722 0.1712 0.1761 0.1919 0.198 33.83
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 5.2516 f_angle_d 0.9622 f_chiral_restr 0.0604 f_bond_d 0.0084 f_plane_restr 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1215 Nucleic Acid Atoms Solvent Atoms 215 Heterogen Atoms 14
Software Software Software Name Purpose PHENIX refinement PHENIX refinement XDS data reduction XSCALE data scaling PHENIX phasing