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Crystal structure of mouse Carboxylesterase 2e (Ces2e)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8AXC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293.15 Protein stock solution in 20 mM Tris/HCl, pH 7.4, and 150 mM NaCl; ShotGun (SG1) Screen: E1 (2.0 M ammonium sulfate and 0.1 M Bis-Tris buffer pH 5.5) with protein end concentration of 2.89 mg/ml in a 0.5 uL drop
Crystal Properties Matthews coefficient Solvent content 2.72 54.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 126.931 α = 90 b = 145.243 β = 90 c = 149.432 γ = 90
Symmetry Space Group C 2 2 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 EIGER2 X 9M 2022-01-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 0.873128 ESRF ID23-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.4 80.646 99.9 0.0755 0.994 9.38 2 54113
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.4 2.486 0.4157 0.723 2.19
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 2.4 80.646 54111 2718 99.856 0.178 0.1756 0.1772 0.2138 0.2146 36.312
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] -1.461 -1.111 2.572
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.213 r_dihedral_angle_4_deg 19.211 r_dihedral_angle_3_deg 13.344 r_lrange_it 10.309 r_lrange_other 10.228 r_dihedral_angle_1_deg 7.041 r_scangle_other 6.504 r_scangle_it 6.499 r_mcangle_it 4.875 r_mcangle_other 4.875
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.213 r_dihedral_angle_4_deg 19.211 r_dihedral_angle_3_deg 13.344 r_lrange_it 10.309 r_lrange_other 10.228 r_dihedral_angle_1_deg 7.041 r_scangle_other 6.504 r_scangle_it 6.499 r_mcangle_it 4.875 r_mcangle_other 4.875 r_scbond_it 4.134 r_scbond_other 4.13 r_mcbond_it 3.018 r_mcbond_other 3.007 r_angle_refined_deg 1.543 r_angle_other_deg 1.301 r_ext_dist_refined_d 0.281 r_nbd_other 0.22 r_nbd_refined 0.194 r_symmetry_nbd_refined 0.189 r_xyhbond_nbd_refined 0.178 r_symmetry_nbd_other 0.171 r_nbtor_refined 0.16 r_symmetry_xyhbond_nbd_refined 0.152 r_ncsr_local_group_1 0.094 r_symmetry_nbtor_other 0.091 r_chiral_restr 0.078 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8154 Nucleic Acid Atoms Solvent Atoms 698 Heterogen Atoms 249
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing