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Arginase from Arabidopsis thaliana in Complex with Ornithine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6VSS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 292 50 mM L-arginine, 50 mM L-glutamic acid, 22% PEG Smear Broad, 5% glycerol
Crystal Properties Matthews coefficient Solvent content 2.8 56.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 267.322 α = 90 b = 267.322 β = 90 c = 262.894 γ = 90
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 EIGER X 16M 2018-06-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.00 APS 22-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.25 30 99 0.064 0.994 17.1 3.3 429624 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.25 2.33 99.9 0.483 0.747 2.5 3.4
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 6VSS 2.25 29.97 424973 2236 98.43 0.1594 0.1592 0.1665 0.1968 0.2019 RANDOM 41.31
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] 0.05 0.05 -0.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.173 r_dihedral_angle_4_deg 17.451 r_dihedral_angle_3_deg 14.846 r_dihedral_angle_1_deg 7.05 r_angle_refined_deg 1.783 r_angle_other_deg 1.412 r_chiral_restr 0.089 r_bond_refined_d 0.014 r_gen_planes_refined 0.009 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.173 r_dihedral_angle_4_deg 17.451 r_dihedral_angle_3_deg 14.846 r_dihedral_angle_1_deg 7.05 r_angle_refined_deg 1.783 r_angle_other_deg 1.412 r_chiral_restr 0.089 r_bond_refined_d 0.014 r_gen_planes_refined 0.009 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 58150 Nucleic Acid Atoms Solvent Atoms 4951 Heterogen Atoms 362
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-3000 data reduction HKL-3000 data scaling PHASER phasing