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Crystal structure reveals non-coordinative binding of O2 to the copper center of the formylglycine-generating enzyme - FGE:Cu:S:O2-1d complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6S07
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 293 7-12 % PEG 8000, 0.2-0.3 M MgCl2, Tris-HCl
Crystal Properties Matthews coefficient Solvent content 2.32 47.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.104 α = 90 b = 72.222 β = 90 c = 76.886 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 2M-F 2019-10-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.0006777109999108 SLS X06SA
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 1.2 46.36 97.5 0.052 0.054 0.015 1 27 12.5 99101 10.76
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 1.2 1.22 99.9 0.783 0.818 0.235 0.933 11.9
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 THROUGHOUT 6S07 1.2 46.356 1.33 98094 4833 96.55 0.2006 0.1998 0.2007 0.2159 0.2175 14.3945
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 8.752 f_angle_d 1.124 f_chiral_restr 0.086 f_plane_restr 0.01 f_bond_d 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2460 Nucleic Acid Atoms Solvent Atoms 385 Heterogen Atoms 7
Software Software Software Name Purpose XDS data reduction Aimless data scaling PHENIX refinement PDB_EXTRACT data extraction PHASER phasing