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Crystal structure of Homo sapiens NUP93 solenoid (residues 174-819)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5HB3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 294 0.075 M TRIS pH 8.5, 19 % (w/v) PEG 20000
Crystal Properties Matthews coefficient Solvent content 2.29 46.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.87 α = 90 b = 66.07 β = 116.275 c = 79.18 γ = 90
Symmetry Space Group P 1 21 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 2018-12-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-2 0.97946 SSRL BL12-2
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 40 99.09 0.088 0.09 0.02 1 26 20.9 46714 42
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.071 98.27 2.537 2.598 0.555 0.733 1.54 21.5
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 5HB3 2 40 1.34 46714 2002 99.03 0.2262 0.2249 0.2544 0.2195 57.45
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 11.971 f_angle_d 0.4518 f_chiral_restr 0.0334 f_plane_restr 0.0025 f_bond_d 0.0024
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5062 Nucleic Acid Atoms Solvent Atoms 192 Heterogen Atoms 4
Software Software Software Name Purpose Blu-Ice data collection XDS data reduction XDS data scaling PHASER phasing PHENIX refinement Coot model building