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Human NUP98 APD (SG P41212)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.8 293 25% PEG 3350
0.2 MgCl2
0.1 M HEPES pH 6.8
Crystal Properties Matthews coefficient Solvent content 2.39 48.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.499 α = 90 b = 60.499 β = 90 c = 89.801 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 EIGER2 XE 16M 2025-06-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97625 Diamond I03
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 1.5 50.17 100 0.125 0.127 0.025 0.999 16.2 26.1 27463
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 1.5 1.53 100 1.765 1.799 0.346 0.835 26.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.5 38.651 27389 1370 99.964 0.192 0.1916 0.1915 0.2055 0.2049 17.612
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] 0.532 0.532 -1.064
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.566 r_dihedral_angle_3_deg 10.79 r_dihedral_angle_1_deg 6.051 r_dihedral_angle_2_deg 5.246 r_lrange_it 4.567 r_lrange_other 4.428 r_scangle_it 3.156 r_scangle_other 3.154 r_mcangle_other 2.198 r_mcangle_it 2.197
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.566 r_dihedral_angle_3_deg 10.79 r_dihedral_angle_1_deg 6.051 r_dihedral_angle_2_deg 5.246 r_lrange_it 4.567 r_lrange_other 4.428 r_scangle_it 3.156 r_scangle_other 3.154 r_mcangle_other 2.198 r_mcangle_it 2.197 r_scbond_it 2.068 r_scbond_other 2.067 r_mcbond_it 1.426 r_mcbond_other 1.412 r_angle_refined_deg 1.377 r_angle_other_deg 0.488 r_symmetry_metal_ion_refined 0.43 r_metal_ion_refined 0.352 r_nbd_refined 0.216 r_symmetry_nbd_refined 0.213 r_symmetry_nbd_other 0.192 r_nbtor_refined 0.178 r_nbd_other 0.16 r_symmetry_xyhbond_nbd_refined 0.139 r_xyhbond_nbd_refined 0.129 r_symmetry_nbtor_other 0.08 r_chiral_restr 0.067 r_xyhbond_nbd_other 0.029 r_bond_refined_d 0.006 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1195 Nucleic Acid Atoms Solvent Atoms 153 Heterogen Atoms 11
Software Software Software Name Purpose REFMAC refinement Aimless data scaling xia2 data reduction MOLREP phasing PDB_EXTRACT data extraction