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Beta-keto acid cleavage enzyme from Paracoccus denitrificans
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3E49
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 289 The enzyme (8.6 mg/mL) in 50 mM HEPES pH 7.8, 150 mM KCl, 1 M L-proline, and 1 mM ZnCl2 was mixed in a 1:1 ratio with 25 % (w/v) pentaerythritol propoxylate (17/8 PO/OH), 100 mM HEPES pH 7.5. The final size of the drops was 1 microliter.
Prior to flash freezing the crystals in liquid nitrogen, the mother liquor was supplemented with 37 % (w/v) pentaerythrol propoxylate (17/8 PO/OH).
Crystal Properties Matthews coefficient Solvent content 2.76 55.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.065 α = 90 b = 137.871 β = 90 c = 132.517 γ = 90
Symmetry Space Group C 2 2 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 EIGER2 X CdTe 16M 2021-08-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2) 0.9763 PETRA III, EMBL c/o DESY P14 (MX2)
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 1.45 24.78 99.1 0.09 0.093 0.026 0.997 19.2 12.1 129609
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 1.45 1.53 95.5 0.499 0.525 0.157 0.929 10.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.45 24.78 1.13 129520 2005 98.95 0.1567 0.1564 0.1581 0.1768 0.1783
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 12.686 f_angle_d 1.425 f_chiral_restr 0.113 f_bond_d 0.015 f_plane_restr 0.014
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4692 Nucleic Acid Atoms Solvent Atoms 822 Heterogen Atoms 18
Software Software Software Name Purpose XDS data reduction SCALA data scaling PHENIX refinement PHENIX phasing