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Crystal structure of D-phenylglycine aninotransferase (D-PhgAT) from Pseudomonas stutzeri with PLP internal aldimine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2CY8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 9.5 298 Yellow crystals, indicating the presence of PLP, were produced by adding 1 uL of 9.1 mg/ml D-PhgAT in 0.1 M CAPS, pH 9.5, 150 mM NaCl, 50 uM PLP to 1 yL of 0.1 M Tris-HCl, pH 7.5, 0.2 M MgCl2, 10 % (w/v) polyethylene glycol 8000.
Crystal Properties Matthews coefficient Solvent content 3.18 61.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 329.28 α = 90 b = 83.9 β = 111.58 c = 133.42 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 PILATUS 6M 2017-02-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.979 Diamond I03
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 2.248 49.47 99.76 0.078 0.091 0.046 0.998 12.1 6.8 160811 49.98
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 2.248 2.28 96.5 0.658 0.895 0.602 0.562 1.5 3.5
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 2CY8 2.248 49.466 1.34 160770 8144 99.77 0.1843 0.1828 0.1865 0.2106 0.2124
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 10.211 f_angle_d 0.543 f_chiral_restr 0.039 f_bond_d 0.003 f_plane_restr 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 20233 Nucleic Acid Atoms Solvent Atoms 409 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing