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STRUCTURE OF ESTER-HYDROLASE EH7 FROM METAGENOME OF MARINE SEDIMENTS AT MILAZZO HARBOR (SICILY, ITALY) COMPLEXED WITH A DERIVATIVE OF METHYL 4-NITROPHENYL HEXYLPHOSPHONATE
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7PP3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 24% PEG3350, 0.1M Bis-Tris propane 8.5, 0.2M NaF
Crystal Properties Matthews coefficient Solvent content 2.41 49.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 150.641 α = 90 b = 150.641 β = 90 c = 325.261 γ = 90
Symmetry Space Group P 43 21 2
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) 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 2.65 49.68 98.4 0.093 0.043 0.998 13 5.4 107165
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 2.65 2.7 98.6 0.69 0.326 0.76 2.5 5.3
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 7PP3 2.65 49.68 101698 5373 98.14 0.1971 0.196 0.199 0.2165 0.2175 RANDOM 44.907
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] 1.52 1.52 -3.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.842 r_dihedral_angle_4_deg 18.079 r_dihedral_angle_3_deg 14.772 r_dihedral_angle_1_deg 6.674 r_angle_refined_deg 1.468 r_angle_other_deg 1.247 r_chiral_restr 0.065 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.842 r_dihedral_angle_4_deg 18.079 r_dihedral_angle_3_deg 14.772 r_dihedral_angle_1_deg 6.674 r_angle_refined_deg 1.468 r_angle_other_deg 1.247 r_chiral_restr 0.065 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 25128 Nucleic Acid Atoms Solvent Atoms 192 Heterogen Atoms 43
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction XDS data scaling MOLREP phasing