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STRUCTURE OF ESTER-HYDROLASE EH1AB1 FROM THE METAGENOME OF LAKE ARREO COMPLEXED WITH A DERIVATIVE OF BIPYRIDINE PHOSPHONATE
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6I8F
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 291 20% PEG 3350, 0.1M Bis-Tris propane pH 7.5, 0.2 M NaF
Crystal Properties Matthews coefficient Solvent content 2.85 56.78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.766 α = 90 b = 201.92 β = 112.19 c = 90.637 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 PILATUS3 S 6M KB focusing mirrors 2019-02-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 0.97926 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 2.79 49.08 99.1 0.277 0.161 0.919 2.7 3.8 37139 51.388
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 2.79 2.91 99.3 0.572 0.327 0.752 1.6 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 (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 6I8F 2.79 49.08 35315 1823 99.06 0.24092 0.23905 0.2406 0.27602 0.2788 RANDOM 48.362
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] 2 -2 1.6 -1.47
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.698 r_dihedral_angle_4_deg 18.196 r_dihedral_angle_3_deg 14.826 r_long_range_B_refined 9.923 r_long_range_B_other 9.919 r_scangle_other 7.299 r_dihedral_angle_1_deg 6.533 r_mcangle_other 5.863 r_mcangle_it 5.862 r_scbond_it 4.639
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.698 r_dihedral_angle_4_deg 18.196 r_dihedral_angle_3_deg 14.826 r_long_range_B_refined 9.923 r_long_range_B_other 9.919 r_scangle_other 7.299 r_dihedral_angle_1_deg 6.533 r_mcangle_other 5.863 r_mcangle_it 5.862 r_scbond_it 4.639 r_scbond_other 4.639 r_mcbond_it 3.846 r_mcbond_other 3.842 r_angle_refined_deg 1.476 r_angle_other_deg 1.251 r_chiral_restr 0.076 r_bond_refined_d 0.007 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 9628 Nucleic Acid Atoms Solvent Atoms 72 Heterogen Atoms 64
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing