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H47Q NicC with 2-mercaptopyridine ligand
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5EOW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 291 0.1 M Hepes, pH 7.5, 15-25% polyethylene glycol (PEG) 3350, and 0.2 M magnesium chloride hexahydrate
Crystal Properties Matthews coefficient Solvent content 2.08 40.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.376 α = 90 b = 69.244 β = 90 c = 115.27 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 183 PIXEL DECTRIS EIGER2 X 16M 2023-04-11 M SINGLE WAVELENGTH 2 1 x-ray 183 PIXEL DECTRIS EIGER2 X 16M 2023-04-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 0.97918 APS 24-ID-C 2 SYNCHROTRON APS BEAMLINE 24-ID-C 1.77120 APS 24-ID-C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.17 59.36 98.56 0.1964 0.997 7.66 6.8 20480 35
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 2.17 2.248 0.724
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.17 59.36 0.46 20468 1893 98.43 0.2469 0.245 0.2829 0.2553 43.7
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 10.7912 f_angle_d 0.4878 f_chiral_restr 0.0397 f_plane_restr 0.0032 f_bond_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2837 Nucleic Acid Atoms Solvent Atoms 115 Heterogen Atoms 60
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling PHASER phasing