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2-amino-3-ketobutyrate CoA ligase from Cupriavidus necator glycine binding form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1FC4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 295 0.2 M Lithium sulfate monohydrate, 0.1 M BIS-TRIS pH 6.5, 25% w/v PEG3350, 3% w/v Dextran sulfate sodium salt (Mr 5000)
Crystal Properties Matthews coefficient Solvent content 2.15 42.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.692 α = 90 b = 101.802 β = 112.983 c = 69.832 γ = 90
Symmetry Space Group P 1 21 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 2019-12-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.0 Photon Factory BL-5A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.5 47.73 99.9 0.997 15.5 6.9 26198 32.67
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.59 0.9
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 1FC4 2.5 47.73 1.37 26174 1272 99.94 0.1713 0.1685 0.1718 0.2273 0.2295 34.18
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 17.4101 f_angle_d 0.8862 f_chiral_restr 0.0515 f_bond_d 0.0072 f_plane_restr 0.0044
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6082 Nucleic Acid Atoms Solvent Atoms 290 Heterogen Atoms 40
Software Software Software Name Purpose PHENIX refinement XDS data reduction SCALA data scaling MOLREP phasing