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Crystal Structure of the Pirin Family Protein Redox-sensitive Bicupin YhaK from Yersinia pestis
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.6 289 0.1 M tri-sodium citrate pH 5.6, 10 %(w/v) PEG4000, 10 %(w/v) isopropanol
Crystal Properties Matthews coefficient Solvent content 2.46 50.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.442 α = 90 b = 66.442 β = 90 c = 122.546 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 315r 2017-06-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97921 APS 19-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.85 50 97.5 0.092 18.2 2.9 50165
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.85 1.88 77.6 0.553 0.589 2.9
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 SAD FREE R-VALUE 1.85 33.31 2.28 49985 2460 97.15 0.1747 0.1668 0.2069 0.2102 29.79
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 5.9982 f_angle_d 0.7337 f_chiral_restr 0.0498 f_plane_restr 0.005 f_bond_d 0.0043
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4360 Nucleic Acid Atoms Solvent Atoms 395 Heterogen Atoms 2
Software Software Software Name Purpose PHENIX refinement SBC-Collect data collection HKL-3000 data scaling HKL-3000 data processing HKL-3000 phasing MLPHARE phasing Coot model building