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NYN domain of human KHNYN complex with RNA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 Tris-HCl, PEG4000, calcium chloride, 1-Propanol
Crystal Properties Matthews coefficient Solvent content 2.83 56.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 111.197 α = 90 b = 111.197 β = 90 c = 111.197 γ = 90
Symmetry Space Group P 41 3 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 EIGER X 9M 2023-06-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 5C (4A) 0.97495 PAL/PLS 5C (4A)
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 1.92 50 99.9 0.999 53.2875 104 18429
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 1.92 1.95 0.424
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 SAD FREE R-VALUE 1.925 49.729 18391 976 99.891 0.181 0.1797 0.1915 0.2094 0.2204 39.22
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 r_dihedral_angle_6_deg 17.229 r_lrange_it 14.463 r_lrange_other 14.46 r_dihedral_angle_3_deg 13.263 r_dihedral_angle_2_deg 13.183 r_scangle_it 10.042 r_scangle_other 10.038 r_dihedral_angle_1_deg 7.146 r_scbond_it 6.277 r_scbond_other 6.273
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.229 r_lrange_it 14.463 r_lrange_other 14.46 r_dihedral_angle_3_deg 13.263 r_dihedral_angle_2_deg 13.183 r_scangle_it 10.042 r_scangle_other 10.038 r_dihedral_angle_1_deg 7.146 r_scbond_it 6.277 r_scbond_other 6.273 r_mcangle_it 6.221 r_mcangle_other 6.218 r_mcbond_it 4.028 r_mcbond_other 4.022 r_angle_refined_deg 1.583 r_angle_other_deg 0.52 r_nbd_other 0.303 r_symmetry_nbd_refined 0.238 r_nbd_refined 0.211 r_symmetry_nbd_other 0.207 r_nbtor_refined 0.183 r_xyhbond_nbd_refined 0.178 r_symmetry_xyhbond_nbd_refined 0.159 r_dihedral_angle_other_2_deg 0.092 r_symmetry_nbtor_other 0.082 r_chiral_restr 0.075 r_bond_refined_d 0.009 r_gen_planes_refined 0.009 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1320 Nucleic Acid Atoms 102 Solvent Atoms 167 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling SHELXD phasing