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Crystal structure of the D183N variant of human Alanine:Glyoxylate Aminotransferase major allele (AGT-Ma) at pH 9.0. 2.8 Ang; internal aldimine with PLP in the active site
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5LUC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 9 294 protein - 15 mg/ml (165 microM) in
40 mM PhO pH 7.4, 60 mM Hepes pH 7.0, 1.6 molar excess PLP
Reservoir - Hampton Research Crystal Screen solution H12 - 2% dioxane, 0.1M bicine pH 9.0, 10% PEG 20K
Mixing - 0.4 + 0.4 microL
Crystal Properties Matthews coefficient Solvent content 3.23 61.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.049 α = 90 b = 89.049 β = 90 c = 140.864 γ = 90
Symmetry Space Group P 41 21 2
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 2016-10-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ELETTRA BEAMLINE 5.2R 1.000 ELETTRA 5.2R
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 2.8 46.95 100 0.087 0.091 0.026 0.997 20.4 12.5 14614
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 2.8 2.95 99.8 1.032 1.078 0.308 0.958 2.5 12.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 THROUGHOUT 5LUC 2.8 46 13721 684 98.8 0.265 0.262 0.2671 0.324 0.3193 RANDOM 89.86
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] 4.99 4.99 -9.99
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2912 Nucleic Acid Atoms Solvent Atoms 29 Heterogen Atoms 6
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing PDB_EXTRACT data extraction