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Crystal structure of human Alanine:Glyoxylate Aminotransferase major allele (AGT-Ma) at 1.7 Angstrom; internal aldimine with PLP in the active site
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1HOC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5 294 Protein solution; 0.2 M AGT, 18mM potassium phosphate pH7.4, 20mM Hepes pH 7.4, 5% Jeffamine (Hampton), 5mM sodium hydroxylamine.
Reservoir; PEG 6k 12%, 100 mM MES pH 5.0.
Mixing: 1+1 microL
Cryoprotectant; 25% MPD
Crystal Properties Matthews coefficient Solvent content 2.14 42.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.479 α = 90 b = 101.88 β = 90 c = 131.338 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 PIXEL DECTRIS PILATUS 2M 2015-03-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ELETTRA BEAMLINE 5.2R 1.00 ELETTRA 5.2R
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.7 48.04 87 0.082 0.042 0.997 10.6 4.2 70070 20.08
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.7 1.73 83.4 0.614 0.324 0.755 1.6 3.9 3510
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 1hoc 1.7 45.118 1.34 70010 3411 86.27 0.1605 0.1583 0.1598 0.2047 0.2054 22.7206
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 14.617 f_angle_d 1.15 f_chiral_restr 0.056 f_bond_d 0.011 f_plane_restr 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5977 Nucleic Acid Atoms Solvent Atoms 802 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement Aimless data scaling MOLREP phasing PDB_EXTRACT data extraction Coot model building XDS data reduction