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Ethylene forming enzyme in complex with manganese, 2-oxoglutarate and N-omega-hydroxy-L-arginine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5V2Z
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 277.15 0.5 ul 72 mg/ml selenomethionine containing EFE (9 mM manganese chloride, 25 mM HEPES pH 8.0, 1 mM TCEP) was mixed with 0.5 ul reservoir solution of 10 mM N-omega-hydroxy-L-arginine, and 0.2 uL of 100 mM 2OG. The sitting drop reservoir of 200 ul contained 20% w/v Polyethylene glycol 6,000, 0.1 M Tris pH 8.0, 0.2 M Lithium chloride. The crystal was soaked for about a minute in 25% w/v ethylene glycol, 75% reservoir solution before freezing it.
Crystal Properties Matthews coefficient Solvent content 2.2 44.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.583 α = 90 b = 82.098 β = 90 c = 87.766 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 CCD MARMOSAIC 300 mm CCD 2017-04-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.9787 APS 21-ID-F
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 1.169 48.58 99.2 0.094 0.103 0.042 0.997 12.3 5.7 118142 9.78
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 1.169 1.19 87.9 0.593 0.687 0.339 0.752 3.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 5V2Z 1.169 38.701 1.9 111915 5867 97.54 0.1732 0.1724 0.1692 0.1876 0.1854 16.2119
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 14.283 f_angle_d 0.961 f_chiral_restr 0.076 f_bond_d 0.009 f_plane_restr 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2728 Nucleic Acid Atoms Solvent Atoms 505 Heterogen Atoms 40
Software Software Software Name Purpose Aimless data scaling PHASER phasing PHENIX refinement PDB_EXTRACT data extraction XDS data reduction