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Crystal Structure of Nup358/RanBP2 Ran-binding domain 4 in complex with Ran-GPPNHP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1RRP PDB entry 1RRP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 294 20% w/v PEG3350, 0.1 M ammonium sulfate, 0.1 M HEPES
Crystal Properties Matthews coefficient Solvent content 2.33 47.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 142.69 α = 90 b = 142.69 β = 90 c = 96.65 γ = 120
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 2021-03-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-2 1.03317 SSRL BL12-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim I (All) Rpim I (All) 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 2.35 29.36 99.9 0.154 0.048 12.4 10.2 91578 47.55
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.35 2.43 99.8 1.835 0.591 1.8 9.5
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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 1RRP 2.35 29.36 1.97 91515 4426 99.87 0.1854 0.1833 0.1833 0.2252 0.2259 66.4518
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]
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 16634 Nucleic Acid Atoms Solvent Atoms 473 Heterogen Atoms 270
Software Software Software Name Purpose xia2 data scaling PHENIX refinement PDB_EXTRACT data extraction Coot model building PHASER phasing XDS data reduction