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Crystal structure of the D183N variant of human Alanine:Glyoxylate Aminotransferase major allele (AGT-Ma) at 1.8 Angstrom; internal aldimine with PLP in the active site
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5F9S
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 294 mixing equal volumes of
protein solution: 15 mg/ml in
40 mM PhO pH 7.4 - 60 mM Hepes pH 7.0
reservoir: ammonium acetate o.1 M - BIS TRIS pH 5.5 0.1M - 17% PEG 10K
Crystal Properties Matthews coefficient Solvent content 3.37 63.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 127.599 α = 90 b = 141.107 β = 90 c = 256.117 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 225 mm CCD 2016-05-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 0.873 ESRF ID23-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.8 57.23 94.2 0.151 0.987 6.2 4.3 397712
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.83 96.1 0.722 0.707 4.1
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 5f9s 1.8 56.692 1.34 397475 19829 93.64 0.1646 0.1631 0.1638 0.1919 0.192 random selection 14.9516
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 16.399 f_angle_d 1.598 f_chiral_restr 0.099 f_bond_d 0.022 f_plane_restr 0.011
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 23741 Nucleic Acid Atoms Solvent Atoms 4154 Heterogen Atoms 112
Software Software Software Name Purpose Aimless data scaling MOLREP phasing PHENIX refinement PDB_EXTRACT data extraction XDS data reduction MOLREP phasing