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STRUCTURE OF ESTER-HYDROLASE EH3 FROM THE METAGENOME OF MARINE SEDIMENTS AT MILAZZO HARBOR (SICILY, ITALY) COMPLEXED WITH A DERIVATIVE OF BIPYRIDINE PHOSPHONATE
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6SXP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 27% PEG3350, 0.1M Bis-Tris pH 6.5
Crystal Properties Matthews coefficient Solvent content 2.36 47.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.755 α = 90 b = 189.39 β = 111.93 c = 75.954 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 PILATUS3 6M KB focusing mirrors 2020-07-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 0.979181 ALBA XALOC
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.4 47.35 100 0.126 0.057 0.993 8.1 5.7 57906
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.4 2.47 100 0.519 0.231 0.884 3.4 5.8
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 (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.4 47.35 54940 2927 99.88 0.24438 0.24394 0.25293 0.2902 RANDOM 42.276
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] 25.04 -8.31 -5.38 -19.66
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.617 r_dihedral_angle_4_deg 20.604 r_dihedral_angle_3_deg 16.463 r_dihedral_angle_1_deg 6.888 r_long_range_B_refined 5.449 r_long_range_B_other 5.447 r_mcangle_it 3.039 r_mcangle_other 3.039 r_scangle_other 2.411 r_mcbond_it 1.829
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.617 r_dihedral_angle_4_deg 20.604 r_dihedral_angle_3_deg 16.463 r_dihedral_angle_1_deg 6.888 r_long_range_B_refined 5.449 r_long_range_B_other 5.447 r_mcangle_it 3.039 r_mcangle_other 3.039 r_scangle_other 2.411 r_mcbond_it 1.829 r_mcbond_other 1.829 r_scbond_it 1.441 r_scbond_other 1.441 r_angle_refined_deg 1.44 r_angle_other_deg 1.193 r_chiral_restr 0.063 r_bond_refined_d 0.005 r_gen_planes_refined 0.005 r_bond_other_d 0.003 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 10266 Nucleic Acid Atoms Solvent Atoms 124 Heterogen Atoms 39
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing