☰ Navigation Tabs
wild-type Formylglycine generating enzyme reacted with iodoacetamide
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 2.27 45.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.058 α = 90 b = 109.788 β = 90 c = 43.461 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 2005-01-28 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 1.54 50 98.5 0.045 41.5 6.6 44155 14.19
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 1.54 1.6 85.5 0.229 4.9 3.7
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 1.54 43.48 41989 2116 99.03 0.15163 0.1504 0.1517 0.17598 0.1776 RANDOM 11.798
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] 0.15 0.22 -0.37
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.195 r_dihedral_angle_4_deg 16.184 r_dihedral_angle_3_deg 12.429 r_dihedral_angle_1_deg 6.458 r_scangle_it 2.688 r_scbond_it 1.766 r_angle_refined_deg 1.306 r_mcangle_it 1.238 r_angle_other_deg 0.843 r_mcbond_it 0.774
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.195 r_dihedral_angle_4_deg 16.184 r_dihedral_angle_3_deg 12.429 r_dihedral_angle_1_deg 6.458 r_scangle_it 2.688 r_scbond_it 1.766 r_angle_refined_deg 1.306 r_mcangle_it 1.238 r_angle_other_deg 0.843 r_mcbond_it 0.774 r_nbd_refined 0.229 r_nbd_other 0.202 r_symmetry_vdw_other 0.201 r_symmetry_hbond_refined 0.199 r_nbtor_refined 0.189 r_symmetry_vdw_refined 0.18 r_mcbond_other 0.178 r_xyhbond_nbd_refined 0.173 r_chiral_restr 0.089 r_nbtor_other 0.081 r_metal_ion_refined 0.027 r_bond_refined_d 0.01 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 2173 Nucleic Acid Atoms Solvent Atoms 523 Heterogen Atoms 34
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling