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Ethylene forming enzyme in complex with manganese, malic acid and L-arginine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5V2T
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 277.15 0.2 ul 64 mg/ml EFE (+1 mM manganese chloride, 25 mM HEPES pH 8.0, 1 mM TCEP, +2.5 mM L-arginine) was mixed with 0.2 ul reservoir solution. The sitting drop reservoir of 50 ul contained 25% PEG 1500 and 0.1 M MMT buffer, pH 6.5. The crystal was soaked for about a minute in 25% w/v Polyethylene glycol 400, 75% reservoir solution before freezing it.
Crystal Properties Matthews coefficient Solvent content 2.89 57.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.36 α = 90 b = 87.36 β = 90 c = 104.3 γ = 120
Symmetry Space Group P 32 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 EIGER X 9M 2017-02-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 1.1272 APS 21-ID-D
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 1.48 61.24 97.9 0.084 0.091 0.033 0.998 12.8 7.2 75179 16.94
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 1.48 1.51 96.4 1.054 1.133 0.409 0.639 7.4 3605
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 5V2T 1.48 43.68 1.92 72267 7113 97.37 0.1365 0.1352 0.1329 0.1621 0.1631 23.777
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 14.85 f_angle_d 1.029 f_chiral_restr 0.078 f_bond_d 0.01 f_plane_restr 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2721 Nucleic Acid Atoms Solvent Atoms 473 Heterogen Atoms 41
Software Software Software Name Purpose MOSFLM data reduction Aimless data scaling PHASER phasing PHENIX refinement PDB_EXTRACT data extraction