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Crystal structure of GAD1 from Arabidopsis thaliana
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1PMM PDB ENTRY 1PMM (E. coli GadB)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 2 uL protein solution (1.9 mg/ml Gad1, 50 mM Hepes pH 7.2, 150 mM NaCl and 10 uM PLP) + 1 uL reservoir solution (100 mM Na acetate pH 5.5, 720 mM Na formate, 9 % PEG 8000 and 9 % PEG 1000), VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.35 47.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 118.098 α = 90 b = 118.098 β = 90 c = 200.576 γ = 120
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 MAR CCD 165 mm DYNAMICALLY BENDABLE MIRROR 2005-02-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 0.90002 SLS X06SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) 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 2.65 30 96.4 0.077 8 2 85232 -3 45.7
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.65 2.74 95.1 0.459 1.7
Refinement Statistics Diffraction ID Structure Solution 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 PDB ENTRY 1PMM (E. coli GadB) 2.672 29.091 1.51 85127 2223 96.15 0.2084 0.208 0.2009 0.2213 0.2138 47.553
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] -8.548 -8.548 17.097
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 14.335 f_angle_d 0.606 f_chiral_restr 0.043 f_bond_d 0.002 f_plane_restr 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 21142 Nucleic Acid Atoms Solvent Atoms 314 Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHENIX refinement PDB_EXTRACT data extraction PHASER phasing