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Alanine-glyoxylate aminotransferase 1 (AGT1) from Arabidopsis thaliana in presence of serine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6PK3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 295 Protein: 11 mg/ml in 20 mM serine, 0.2 mM pyridoxal-phosphate, 10% glycerol, 100 mM Tris-HCl, pH 8.5. Precipitant: 4.1-4.2 M sodium formate, 20 mM serine. One microliter protein + 1 microliter precipitant equilibrated against precipitant.
Crystal Properties Matthews coefficient Solvent content 2.4 48.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 139.179 α = 90 b = 62.376 β = 90 c = 96.982 γ = 90
Symmetry Space Group P 21 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 295 IMAGE PLATE RIGAKU RAXIS IV 2001-02-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RUH2R 1.5418
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 2.1 22.16 90.5 0.1 0.11 0.04 0.99 16 5 236629 45371 19.62
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 2.1 2.14 49.6 0.263 0.32 0.178 0.903 2.3
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 FOURIER SYNTHESIS FREE R-VALUE 6PK3 2.1 22.16 1 45360 3184 90.63 0.1187 0.1151 0.1153 0.1661 0.1653 Random 25.96
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 11.1837 f_angle_d 1.1319 f_chiral_restr 0.074 f_bond_d 0.0148 f_plane_restr 0.0083
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6190 Nucleic Acid Atoms Solvent Atoms 422 Heterogen Atoms 39
Software Software Software Name Purpose CNS refinement PHENIX refinement PDB_EXTRACT data extraction DENZO data reduction SCALEPACK data scaling