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X-ray structure of a truncated mutant of the metallochaperone CooJ with a high-affinity nickel-binding site
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 294 protein concentration of 10 mgmL-1 and 1 equivalent of Ni(II) per dimer, crystals were grown in 16% PEG3350 and 0.2 M calcium chloride
Crystal Properties Matthews coefficient Solvent content 2.05 40.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.8 α = 90 b = 74.28 β = 92.74 c = 70.64 γ = 90
Symmetry Space Group P 1 21 1
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 PILATUS3 6M 2017-11-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID30B 0.97856 ESRF ID30B
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 2.04 46.746 99.2 0.14 0.997 9.4 6.4 30586 1.5 31.4
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 2.04 2.16 96 0.88 0.691 1.63 6.2
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 SAD FREE R-VALUE 2.042 46.746 1.35 30586 1409 99.31 0.2024 0.1996 0.2004 0.2585 0.2597
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 15.152 f_angle_d 1 f_chiral_restr 0.04 f_bond_d 0.007 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3768 Nucleic Acid Atoms Solvent Atoms 300 Heterogen Atoms 63
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling SHELXD phasing