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Formylglycine generating enzyme C336S mutant covalently bound to substrate peptide CTPSR
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1Y1E PDB entry 1Y1E
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 PEG 4000, Calcium chloride, TRIS, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.25 45.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.64 α = 90 b = 109.592 β = 90 c = 43.456 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 IMAGE PLATE MARRESEARCH 2005-04-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.55 30 97.5 0.033 41.2 4.3 42603 16.43
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.55 1.61 89.3 0.181 5.6 3.2
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 PDB entry 1Y1E 1.55 24.5 40491 2063 97.43 0.14601 0.14442 0.1514 0.17777 0.188 RANDOM 18.218
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] 0.14 0.44 -0.57
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.023 r_dihedral_angle_4_deg 15.761 r_dihedral_angle_3_deg 12.418 r_dihedral_angle_1_deg 6.432 r_scangle_it 2.895 r_scbond_it 1.932 r_angle_refined_deg 1.408 r_mcangle_it 1.374 r_mcbond_it 0.906 r_angle_other_deg 0.843
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.023 r_dihedral_angle_4_deg 15.761 r_dihedral_angle_3_deg 12.418 r_dihedral_angle_1_deg 6.432 r_scangle_it 2.895 r_scbond_it 1.932 r_angle_refined_deg 1.408 r_mcangle_it 1.374 r_mcbond_it 0.906 r_angle_other_deg 0.843 r_mcbond_other 0.231 r_nbd_refined 0.217 r_symmetry_vdw_other 0.205 r_nbd_other 0.204 r_symmetry_hbond_refined 0.192 r_nbtor_refined 0.188 r_xyhbond_nbd_refined 0.167 r_symmetry_vdw_refined 0.167 r_chiral_restr 0.09 r_nbtor_other 0.085 r_metal_ion_refined 0.083 r_bond_refined_d 0.012 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.002 r_xyhbond_nbd_other r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2214 Nucleic Acid Atoms Solvent Atoms 531 Heterogen Atoms 31
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling