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STRUCTURE OF ESTER-HYDROLASE EH3 FROM THE METAGENOME OF MARINE SEDIMENTS AT MILAZZO HARBOR (SICILY, ITALY)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5HC0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 24% PEG 3000, 0.2M MgCl2, 0.1M Bis-Tris pH 6.5
Crystal Properties Matthews coefficient Solvent content 2.26 45.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 183.296 α = 90 b = 51.615 β = 93.86 c = 70.254 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 2017-07-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 1.07218 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 2.15 45.76 100 0.15 0.068 0.992 8.6 5.5 36003
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 2.15 2.22 99.9 0.648 0.294 0.88 3.4 5.6
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5HC0 2.15 45.72 34279 1723 99.92 0.203 0.2017 0.2284 0.2364 RANDOM 24.033
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] 2.96 -1.04 -1.48 -1.33
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.225 r_dihedral_angle_4_deg 19.198 r_dihedral_angle_3_deg 14.054 r_dihedral_angle_1_deg 6.35 r_angle_refined_deg 1.388 r_angle_other_deg 1.284 r_chiral_restr 0.066 r_bond_refined_d 0.005 r_gen_planes_refined 0.005 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.225 r_dihedral_angle_4_deg 19.198 r_dihedral_angle_3_deg 14.054 r_dihedral_angle_1_deg 6.35 r_angle_refined_deg 1.388 r_angle_other_deg 1.284 r_chiral_restr 0.066 r_bond_refined_d 0.005 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5109 Nucleic Acid Atoms Solvent Atoms 312 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction Aimless data scaling MOLREP phasing