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Structure of Lentithecium fluviatile carbohydrate esterase from the CE15 family (LfCE15C)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3PIC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277.15 Protein stock: 13.7 mg/mL in 20 mM Tris pH 8.0
Reservoir: 0.2 M Ammonium formate pH 6.6, 20 %w/v PEG 3350
Drop: 3:1 protein to reservoir ratio
Crystal Properties Matthews coefficient Solvent content 2.51 51.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.74 α = 113.322 b = 79.57 β = 98.531 c = 86.01 γ = 94.44
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 EIGER X 16M 2018-06-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX IV BEAMLINE BioMAX 0.980779 MAX IV BioMAX
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.65 47.254 97.4 0.982 4.3 3.8 47781
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.65 2.72 97.2 0.513 1 3.9
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3PIC 2.65 47.254 47781 2294 97.626 0.241 0.2379 0.2412 0.2977 0.3041 59.101
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] 4.938 -2.676 5.124 -2.868 -2.909 -0.623
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.509 r_dihedral_angle_4_deg 18.085 r_dihedral_angle_3_deg 17.73 r_dihedral_angle_other_3_deg 13.788 r_lrange_it 11.823 r_lrange_other 11.821 r_dihedral_angle_1_deg 7.225 r_scangle_it 7.042 r_scangle_other 7.041 r_mcangle_it 6.859
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.509 r_dihedral_angle_4_deg 18.085 r_dihedral_angle_3_deg 17.73 r_dihedral_angle_other_3_deg 13.788 r_lrange_it 11.823 r_lrange_other 11.821 r_dihedral_angle_1_deg 7.225 r_scangle_it 7.042 r_scangle_other 7.041 r_mcangle_it 6.859 r_mcangle_other 6.858 r_scbond_it 4.583 r_scbond_other 4.583 r_mcbond_it 4.419 r_mcbond_other 4.418 r_angle_refined_deg 1.448 r_angle_other_deg 1.183 r_nbd_other 0.28 r_symmetry_nbd_refined 0.203 r_nbd_refined 0.199 r_symmetry_xyhbond_nbd_refined 0.193 r_symmetry_nbd_other 0.187 r_xyhbond_nbd_refined 0.169 r_nbtor_refined 0.164 r_symmetry_xyhbond_nbd_other 0.091 r_symmetry_nbtor_other 0.085 r_ncsr_local_group_1 0.07 r_ncsr_local_group_5 0.066 r_ncsr_local_group_4 0.064 r_ncsr_local_group_2 0.06 r_chiral_restr 0.057 r_ncsr_local_group_3 0.055 r_ncsr_local_group_6 0.046 r_bond_refined_d 0.006 r_gen_planes_refined 0.005 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11382 Nucleic Acid Atoms Solvent Atoms 303 Heterogen Atoms 250
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing