☰ Navigation Tabs
Formylglycine generating enzyme C336S mutant covalently bound to substrate peptide LCTPSRA
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 45.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.719 α = 90 b = 109.517 β = 90 c = 43.52 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 2005-07-20 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 1.73 30 97.8 0.071 29.9 10.2 31093
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 1.73 1.79 87 0.373 1.8 3.1
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 1.73 29.71 29545 1503 98.43 0.14228 0.14068 0.1529 0.17427 0.1855 RANDOM 22.391
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] 0.04 0.63 -0.67
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.06 r_dihedral_angle_4_deg 16.901 r_dihedral_angle_3_deg 12.195 r_dihedral_angle_1_deg 6.558 r_scangle_it 2.897 r_scbond_it 1.954 r_mcangle_it 1.389 r_angle_refined_deg 1.34 r_mcbond_it 0.935 r_angle_other_deg 0.826
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.06 r_dihedral_angle_4_deg 16.901 r_dihedral_angle_3_deg 12.195 r_dihedral_angle_1_deg 6.558 r_scangle_it 2.897 r_scbond_it 1.954 r_mcangle_it 1.389 r_angle_refined_deg 1.34 r_mcbond_it 0.935 r_angle_other_deg 0.826 r_mcbond_other 0.226 r_nbd_refined 0.206 r_symmetry_hbond_refined 0.2 r_nbd_other 0.197 r_nbtor_refined 0.183 r_xyhbond_nbd_refined 0.182 r_symmetry_vdw_other 0.181 r_symmetry_vdw_refined 0.114 r_chiral_restr 0.085 r_nbtor_other 0.083 r_metal_ion_refined 0.078 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 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 2222 Nucleic Acid Atoms Solvent Atoms 495 Heterogen Atoms 31
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling