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Crystal Structure of Arabidopsis thaliana Agmatine Deiminase from Cell Free Expression
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 Protein solution- 10 mg/ml agmatine deiminase, 50 mM NaCl, 0.3 mM TCEP, 5 mM HEPES, pH 7.0; Precipitant solution- 34% Polyethylene glycol 2000, 200 mM KBr, 100 mM triethanolamine, pH 7.5; Cryoprotectant- MiTeGen LV Cryo Oil, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.51 50.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 123.715 α = 90 b = 69.932 β = 98.4 c = 50.917 γ = 90
Symmetry Space Group C 1 2 1
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 MARMOSAIC 300 mm CCD 2009-04-06 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 0.96350,0.97943,0.97957 APS 23-ID-D
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.5 50 100 0.098 19.6 7.5 68398 68398
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.5 1.53 100 0.444 4.1 6.7 3395
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 MAD THROUGHOUT 1.5 50 68375 3460 99.75 0.147 0.146 0.1488 0.174 0.1686 RANDOM 14.686
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] -0.41 -0.37 0.65 -0.34
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.777 r_dihedral_angle_4_deg 18.289 r_dihedral_angle_3_deg 13.184 r_dihedral_angle_1_deg 7.044 r_scangle_it 5.677 r_scbond_it 3.598 r_mcangle_it 2.519 r_angle_refined_deg 1.63 r_mcbond_it 1.541 r_chiral_restr 0.131
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.777 r_dihedral_angle_4_deg 18.289 r_dihedral_angle_3_deg 13.184 r_dihedral_angle_1_deg 7.044 r_scangle_it 5.677 r_scbond_it 3.598 r_mcangle_it 2.519 r_angle_refined_deg 1.63 r_mcbond_it 1.541 r_chiral_restr 0.131 r_gen_planes_refined 0.018 r_bond_refined_d 0.017
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3073 Nucleic Acid Atoms Solvent Atoms 372 Heterogen Atoms 30
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling RESOLVE phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling AutoSol phasing