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Formylglycine Generating Enzyme from Streptomyces coelicolor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1Y1E
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 100 mM Tris, 2.4 M ammonium formate, 0.3% -octylglucoside, 3.2% 2-butanol, pH 8.0, VAPOR DIFFUSION, HANGING DROP
Crystal Properties Matthews coefficient Solvent content 3.39 63.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 142.444 α = 90 b = 142.444 β = 90 c = 217.067 γ = 120
Symmetry Space Group P 31 2 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 CCD ADSC QUANTUM 315 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.2 ALS 8.2.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.1 20 123276
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.17
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 THROUGHOUT 1Y1E 2.1 20 117425 6203 83.35 0.20106 0.19895 0.2336 0.24114 0.2693 RANDOM 41.231
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] 2.37 1.19 2.37 -3.56
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 25.921 r_dihedral_angle_4_deg 20.617 r_dihedral_angle_3_deg 13.894 r_dihedral_angle_1_deg 5.905 r_sphericity_free 2.348 r_scangle_it 1.163 r_angle_refined_deg 1.099 r_scbond_it 0.797 r_sphericity_bonded 0.571 r_rigid_bond_restr 0.518
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 25.921 r_dihedral_angle_4_deg 20.617 r_dihedral_angle_3_deg 13.894 r_dihedral_angle_1_deg 5.905 r_sphericity_free 2.348 r_scangle_it 1.163 r_angle_refined_deg 1.099 r_scbond_it 0.797 r_sphericity_bonded 0.571 r_rigid_bond_restr 0.518 r_mcangle_it 0.422 r_nbtor_refined 0.301 r_mcbond_it 0.283 r_symmetry_hbond_refined 0.216 r_nbd_refined 0.186 r_xyhbond_nbd_refined 0.153 r_symmetry_vdw_refined 0.124 r_metal_ion_refined 0.119 r_chiral_restr 0.075 r_bond_refined_d 0.008 r_gen_planes_refined 0.003 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11130 Nucleic Acid Atoms Solvent Atoms 976 Heterogen Atoms 5
Software Software Software Name Purpose REFMAC refinement