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Crystal structure of human NIPBL C-terminal domain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 3(M) Ammonium sulphate, 100mM MES pH - 6.5
Crystal Properties Matthews coefficient Solvent content 1.95 36.78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 36.09 α = 90 b = 57.42 β = 90 c = 95.97 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 Bruker PHOTON III HELIOS multilayer optics 2024-01-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SEALED TUBE BRUKER IMUS DIAMOND MICROFOCUS 1.54
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 2.1 49.27 99.93 0.2948 0.3177 0.1177 0.986 5.76 7.2 12202 22.69
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.31 99.83 1.106 0.4799 0.596 1.36 6.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.1 49.27 1.34 12202 611 99.93 0.1995 0.1968 0.1971 0.2502 0.2495 25.86
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 17.9377 f_angle_d 0.8796 f_chiral_restr 0.0519 f_bond_d 0.007 f_plane_restr 0.0062
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1598 Nucleic Acid Atoms Solvent Atoms 149 Heterogen Atoms 50
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PHASER phasing