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Crystal structure of a two-domain esterase (CEX) active on acetylated mannans co-crystallized with mannopentaose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6HFZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 295 0.2 M ammonium acetate, 0.1 M HEPES pH 7.5 and 25% w/v PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.38 48.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.482 α = 90 b = 136.69 β = 113.86 c = 85.411 γ = 90
Symmetry Space Group P 1 21 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 PILATUS 6M 2018-05-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.97625 ESRF ID23-1
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 48.57 98.7 0.097 0.995 8.2 3.5 61043
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 2.53 99.2 0.593 0.713 2 3.5
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 6HFZ 2.4 47.84 57988 3029 98.64 0.18406 0.18057 0.1868 0.25331 0.2578 RANDOM 50.77
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] -1.39 0.74 0.25 0.35
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.054 r_dihedral_angle_3_deg 16.171 r_dihedral_angle_4_deg 14.167 r_long_range_B_refined 7.263 r_long_range_B_other 7.256 r_dihedral_angle_1_deg 7.056 r_scangle_other 4.936 r_mcangle_it 4.623 r_mcangle_other 4.623 r_scbond_it 3.226
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.054 r_dihedral_angle_3_deg 16.171 r_dihedral_angle_4_deg 14.167 r_long_range_B_refined 7.263 r_long_range_B_other 7.256 r_dihedral_angle_1_deg 7.056 r_scangle_other 4.936 r_mcangle_it 4.623 r_mcangle_other 4.623 r_scbond_it 3.226 r_scbond_other 3.223 r_mcbond_it 3.096 r_mcbond_other 3.091 r_angle_refined_deg 1.187 r_angle_other_deg 0.814 r_chiral_restr 0.054 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11568 Nucleic Acid Atoms Solvent Atoms 487 Heterogen Atoms 147
Software Software Software Name Purpose REFMAC refinement PHASER phasing SCALA data scaling XDS data reduction