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human formylglycine-generating enzyme FGE, with surface loop and active site Cu(I)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1Z70
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 9 293.15 0.25 M Tris-HCl pH 9.0, 0.2 M CaCl2, 26 % PEG 4000, 2.5 % DMSO, 200 nl protein + 100 nl reservoir
Crystal Properties Matthews coefficient Solvent content 2.02 39.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.38 α = 90 b = 109.438 β = 90 c = 43.35 γ = 90
Symmetry Space Group P 21 21 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 PILATUS3 2M 2021-11-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.2 0.9184 BESSY 14.2
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 1.15 19.16 98.5 0.196 0.208 0.069 0.998 8.26 8.6 102967
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 1.15 1.19 95.1 2.93 3.11 1.03 0.214 0.58 8.6
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.15 19.16 1.33 102888 5147 98.49 0.1543 0.1531 0.1535 0.1762 0.1766 Random selection 19.94
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 13.2316 f_angle_d 1.1129 f_chiral_restr 0.0852 f_plane_restr 0.0107 f_bond_d 0.0074
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2304 Nucleic Acid Atoms Solvent Atoms 405 Heterogen Atoms 43
Software Software Software Name Purpose XDS data reduction PHASER phasing PHENIX refinement Coot model building