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Crystal structure of Nucleoporin-98 nanobody MS98-6 complex solved at 2.2A resolution
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 9 291 2.5% (w/v) PEG 6000, 25% (v/v) PEG MME 500, 0.1 M Tris-HCl pH 9.0
Crystal Properties Matthews coefficient Solvent content 3.32 58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.76 α = 90 b = 96.63 β = 90 c = 100.87 γ = 90
Symmetry Space Group P 21 21 21
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 2018-11-12 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) 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 48.3 87.7 0.99 17.9 13.2 49105 39.94
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.05 44 0.32 4.98
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 5E0Q 2.2 29.69 1.36 41328 2066 97.93 0.1789 0.1764 0.226 0.1947 56.2
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 3.271 f_angle_d 0.806 f_chiral_restr 0.0537 f_bond_d 0.0067 f_plane_restr 0.0046
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4322 Nucleic Acid Atoms Solvent Atoms 324 Heterogen Atoms 11
Software Software Software Name Purpose PHENIX refinement PHENIX refinement XDS data reduction XSCALE data scaling PHENIX phasing