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Crystal structure of human NIF3L1 protein with hexamer in ASU
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other our previously determined NIF3 structure
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 1.6 M Ammonium sulfate 0.1 M MES 6.5
Crystal Properties Matthews coefficient Solvent content 2.62 53.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.406 α = 90 b = 108.773 β = 90 c = 245.034 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 2M 2021-02-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 1 SLS X06DA
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 3 48.2 99.96 0.972 4.91 5.3 122851
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 3 3.06 0.129 0.44
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 3 48.2 1.34 52415 2533 99.96 0.2069 0.2049 0.2046 0.2458 0.2449
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 6.39 f_angle_d 1.015 f_chiral_restr 0.059 f_plane_restr 0.011 f_bond_d 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 16356 Nucleic Acid Atoms Solvent Atoms 15 Heterogen Atoms 66
Software Software Software Name Purpose PHENIX refinement PDB_EXTRACT data extraction XDS data reduction XDS data scaling PHASER phasing