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Co-crystal structure of UPF3B-RRM-NOPS-L with UPF2-MIF4GIII
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1UW4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 293.15 0.1M Ca acetate
0.1M MES
15% PEG 400 P 41 2 2
Crystal Properties Matthews coefficient Solvent content 2.04 39.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 130.593 α = 90 b = 130.593 β = 90 c = 267.33 γ = 90
Symmetry Space Group P 41 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 277 PIXEL DECTRIS PILATUS 6M-F 2020-06-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.9795 Diamond I04-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.309 30 99.94 0.061 10.2 14.2 80565 53.53
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.55 100 0.809 1 14.4
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 1uw4 2.6 30 1.35 71733 3567 99.94 0.2187 0.2167 0.2175 0.2559 0.2575 60.92
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 10.1195 f_angle_d 0.5363 f_chiral_restr 0.041 f_bond_d 0.0039 f_plane_restr 0.0034
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12043 Nucleic Acid Atoms Solvent Atoms 160 Heterogen Atoms 45
Software Software Software Name Purpose PHENIX refinement PHASER phasing PDB_EXTRACT data extraction XDS data reduction XDS data scaling