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Artificial metalloenzyme with a nickel-based 1,10-phenanthroline cofactor and streptavidin N49M-S112V mutant
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8P5Y
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291.15 11% w/v PEG 8000 0.1M MES 6.0 0.24M Ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 2.49 47.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.46 α = 90 b = 57.46 β = 90 c = 172.46 γ = 90
Symmetry Space Group I 41 2 2
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 2024-05-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-3 0.9655 ESRF MASSIF-3
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim 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 1.27 54.51 97.7 0.044 0.99 17.2 4.7 37345 17.8
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.27 1.3 0.759 0.746 2.1 4.3
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 1.27 54.51 1.35 37338 1859 97.64 0.1782 0.1772 0.1792 0.1965 0.1964 29.76
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 18.1177 f_angle_d 2.275 f_chiral_restr 0.0965 f_bond_d 0.0087 f_plane_restr 0.0079
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 909 Nucleic Acid Atoms Solvent Atoms 36 Heterogen Atoms 70
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing