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Ni-bound crystal structure of the engineered cyt cb562 variant, DiCyt2, crystallized in the presence of Cu(II) (M1) and Ni(II) (M2)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2BC5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.4 293 PEG1500 25%, Ammonium acetate 200 mM, pH 8.4 EPPS 100 mM
Crystal Properties Matthews coefficient Solvent content 2.25 45.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.76 α = 90 b = 61 β = 90 c = 64.16 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 6M 2020-07-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 1.48 SSRL BL9-2
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 1.7 41.65 99.54 0.7754 0.79 0.1475 0.73 49.46 28.4 24213 17.98
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 1.7 1.761 99.37 0.8503 0.8665 0.1641 0.771 8.63 26.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 2bc5 1.7 41.65 1.34 24165 3769 98.99 0.1831 0.1802 0.1842 0.2141 0.2174 21.82
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 11.6716 f_angle_d 0.7751 f_chiral_restr 0.0402 f_bond_d 0.0064 f_plane_restr 0.0054
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1716 Nucleic Acid Atoms Solvent Atoms 245 Heterogen Atoms 2
Software Software Software Name Purpose PHENIX refinement iMOSFLM data reduction Aimless data scaling PHASER phasing