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Crystal structure of mouse Carboxylesterase 2b (Ces2b)
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 7.4 293.15 H2 Morpheus II screen (40 mM polyamines (0.1 M spermine tetrahydrochloride, 0.1 M spermidine trihydrochloride, 0.1 M 1,4-diaminobutane dihydrochloride, 0.1 M DL-ornithine monohydrochloride), 0.1 M buffer system 4 at pH 6.5 (1 M MOPSO, Bis-Tris), and 32.5% v/v precipitant mix 6 (25% w/v PEG 4000, 40% w/v 1,2,6-hexanetriol))
Crystal Properties Matthews coefficient Solvent content 2.67 53.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 180.75 α = 90 b = 109.801 β = 92.886 c = 135.435 γ = 90
Symmetry Space Group C 1 2 1
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 16M 2021-11-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, DESY BEAMLINE P11 1.033190 PETRA III, DESY P11
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim 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 2.55 46.91 99.26 0.08605 0.09302 0.03497 0.998 15.26 7 85640 60.07
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.55 2.641 99.93 0.7941 0.8556 0.316 0.862 2.66 7.3
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.55 46.905 85632 4466 99.277 0.173 0.1709 0.2049 0.2011 69.146
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] -0.066 0.021 0.052 0.012
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.881 r_dihedral_angle_3_deg 14.098 r_lrange_it 11.378 r_scangle_it 8.285 r_dihedral_angle_2_deg 7.086 r_dihedral_angle_1_deg 6.616 r_mcangle_it 6.08 r_scbond_it 5.818 r_mcbond_it 4.016 r_angle_refined_deg 1.805
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.881 r_dihedral_angle_3_deg 14.098 r_lrange_it 11.378 r_scangle_it 8.285 r_dihedral_angle_2_deg 7.086 r_dihedral_angle_1_deg 6.616 r_mcangle_it 6.08 r_scbond_it 5.818 r_mcbond_it 4.016 r_angle_refined_deg 1.805 r_nbtor_refined 0.305 r_symmetry_nbd_refined 0.288 r_nbd_refined 0.215 r_symmetry_xyhbond_nbd_refined 0.182 r_xyhbond_nbd_refined 0.153 r_chiral_restr 0.125 r_ncsr_local_group_1 0.098 r_ncsr_local_group_5 0.097 r_ncsr_local_group_2 0.096 r_ncsr_local_group_6 0.094 r_ncsr_local_group_3 0.087 r_ncsr_local_group_4 0.08 r_gen_planes_refined 0.008 r_bond_refined_d 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 16234 Nucleic Acid Atoms Solvent Atoms 571 Heterogen Atoms 62
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing