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STRUCTURE OF ESTER-HYDROLASE EH1AB1 FROM THE METAGENOME OF LAKE ARREO COMPLEXED WITH A DERIVATIVE OF BUTYL 4-NITROPHENYL HEXYLPHOSPHONATE
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5JD4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 291 45 % PEG P400, 0.1 M BIS-TRIS pH 6.5
Crystal Properties Matthews coefficient Solvent content 2.73 55.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.25 α = 90 b = 88.161 β = 90 c = 98.498 γ = 90
Symmetry Space Group P 21 21 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 PILATUS3 S 6M KB focusing mirrors 2018-09-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 0.97924 ALBA XALOC
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 3.2 49.25 96.5 0.218 0.25 0.119 0.912 4.5 4.1 12184 43.084
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 3.2 3.42 96.2 0.525 0.609 0.298 0.675 2.2 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 5JD4 3.2 49.25 11539 622 95.31 0.22972 0.22733 0.2341 0.27593 0.2831 RANDOM 40.16
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] 2.85 -3.76 0.91
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.232 r_dihedral_angle_4_deg 17.248 r_dihedral_angle_3_deg 13.342 r_dihedral_angle_1_deg 6.188 r_long_range_B_refined 6.139 r_long_range_B_other 6.139 r_scangle_other 3.195 r_mcangle_it 2.786 r_mcangle_other 2.786 r_scbond_it 1.857
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.232 r_dihedral_angle_4_deg 17.248 r_dihedral_angle_3_deg 13.342 r_dihedral_angle_1_deg 6.188 r_long_range_B_refined 6.139 r_long_range_B_other 6.139 r_scangle_other 3.195 r_mcangle_it 2.786 r_mcangle_other 2.786 r_scbond_it 1.857 r_scbond_other 1.857 r_mcbond_it 1.587 r_mcbond_other 1.583 r_angle_refined_deg 1.057 r_angle_other_deg 1.014 r_chiral_restr 0.061 r_bond_refined_d 0.005 r_gen_planes_refined 0.003 r_gen_planes_other 0.002 r_bond_other_d 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 4771 Nucleic Acid Atoms Solvent Atoms 41 Heterogen Atoms 79
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing