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Ni-bound crystal structure of the engineered cyt cb562 variant, DiCyt2, crystallized in the presence of Ni(II) (M1) and Cu(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 8 293 PEG1500 25%, pH 8 EPPS 100 mM, No salt,
Crystal Properties Matthews coefficient Solvent content 2.1 41.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.63 α = 90 b = 60.92 β = 90 c = 63.16 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 2019-10-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 1.03 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 41.32 99.5 0.7238 0.7335 0.1161 0.878 35.1 38.7 23765 17.96
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 99.62 0.9307 0.9442 0.156 0.727 6.5 36.7
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 41.32 1.39 23704 3749 98.85 0.1926 0.1893 0.192 0.2296 0.2325 20.56
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 11.8006 f_angle_d 0.8022 f_chiral_restr 0.0393 f_bond_d 0.0068 f_plane_restr 0.0049
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1720 Nucleic Acid Atoms Solvent Atoms 174 Heterogen Atoms 2
Software Software Software Name Purpose PHENIX refinement iMOSFLM data reduction Aimless data scaling PHASER phasing