☰ Navigation Tabs
Structure of human Alanine:Glyoxylate Aminotransferase major allele (AGT-Ma) showing X-Ray induced reduction of PLP internal aldimine to 4'-deoxy-piridoxine-phosphate (PLR)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1H0C
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 2.15 42.78
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 1.0 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 95.6 0.093 0.05 0.995 9 3.9 77240 20.49
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 90.3 0.659 0.374 0.683 1.3 3.6 3812
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 1H0C 1.7 40.223 1.34 77182 3791 95.11 0.1657 0.1636 0.1654 0.2051 0.2077 22.5215
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 13.798 f_angle_d 1.156 f_chiral_restr 0.058 f_bond_d 0.012 f_plane_restr 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5947 Nucleic Acid Atoms Solvent Atoms 802 Heterogen Atoms 50
Software Software Software Name Purpose Aimless data scaling MOLREP phasing PHENIX refinement PDB_EXTRACT data extraction XDS data reduction