☰ Navigation Tabs
The glucuronyl esterase OtCE15A from Opitutus terrae in complex with a heptasaccharide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6T0I
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 298 OtCE15A mixed 3:1 with reservoir containing 0.10 M Carboxylic acids (0.2M Sodium formate; 0.2M Ammonium acetate; 0.2M Sodium citrate tribasic dihydrate; 0.2M Potassium sodium tartrate tetrahydrate; 0.2M Sodium oxamate), 0.1 M Buffer system 1, pH 6.5 (Imidazole; MES monohydrate (acid)), 37.50 % v/v, Precipitant Mix 4 (25% v/v MPD; 25% PEG 1000; 25% w/v PEG 3350). Solid oligosaccharide added to the drop and soaked for 15 min.
Crystal Properties Matthews coefficient Solvent content 2.24 45.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.77 α = 90 b = 65.43 β = 90 c = 118.62 γ = 90
Symmetry Space Group P 21 21 21
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 6M 2022-09-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, DESY BEAMLINE P11 1.03285 PETRA III, DESY P11
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim 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 2.4 38.6 92.3 0.184 0.993 11.15 4.567 14772
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.4 2.47 78 0.718 0.786 2.42 3.59
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.403 38.599 14772 761 92.244 0.172 0.1676 0.1753 0.2451 0.2553 35.295
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] -1.981 2.421 -0.441
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.781 r_dihedral_angle_6_deg 15.305 r_dihedral_angle_1_deg 7.092 r_dihedral_angle_2_deg 6.174 r_lrange_other 5.843 r_lrange_it 5.84 r_scangle_it 4.249 r_scangle_other 4.249 r_mcangle_other 3.417 r_mcangle_it 3.413
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.781 r_dihedral_angle_6_deg 15.305 r_dihedral_angle_1_deg 7.092 r_dihedral_angle_2_deg 6.174 r_lrange_other 5.843 r_lrange_it 5.84 r_scangle_it 4.249 r_scangle_other 4.249 r_mcangle_other 3.417 r_mcangle_it 3.413 r_scbond_it 2.627 r_scbond_other 2.626 r_mcbond_it 2.171 r_mcbond_other 2.17 r_angle_refined_deg 1.343 r_angle_other_deg 0.473 r_symmetry_nbd_other 0.211 r_nbd_refined 0.21 r_nbtor_refined 0.179 r_nbd_other 0.17 r_metal_ion_refined 0.162 r_xyhbond_nbd_refined 0.151 r_symmetry_xyhbond_nbd_refined 0.104 r_symmetry_nbtor_other 0.082 r_chiral_restr 0.069 r_symmetry_nbd_refined 0.047 r_bond_refined_d 0.005 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3055 Nucleic Acid Atoms Solvent Atoms 119 Heterogen Atoms 69
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing