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Crystal structure of argininosuccinate lyase from Arabidopsis thaliana (AtASL)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2E9F provided from Balbes in CCP4Online
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 294 0.1M BIS-TRIS pH 5.5, 2.0M Ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 3.33 63.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 106.044 α = 90 b = 229.542 β = 90.56 c = 111.586 γ = 90
Symmetry Space Group P 1 21 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 PIXEL DECTRIS EIGER X 16M 2023-05-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX IV BEAMLINE BioMAX 0.976 MAX IV BioMAX
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 1.55 48.48 94.1 0.049 0.061 0.99 13 2.5 720570
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.55 1.61 96.4 0.606 0.775 0.55 1.9
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 MOLECULAR REPLACEMENT THROUGHOUT 1.55 48.45 716967 3603 94.1 0.14714 0.14702 0.1611 0.17118 0.1828 RANDOM 22.517
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] -1.9 0.6 0.64 1.25
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.459 r_long_range_B_refined 8.17 r_long_range_B_other 7.808 r_dihedral_angle_2_deg 5.702 r_dihedral_angle_1_deg 5.319 r_scangle_other 3.788 r_scbond_it 2.707 r_scbond_other 2.51 r_angle_refined_deg 1.935 r_mcangle_it 1.583
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.459 r_long_range_B_refined 8.17 r_long_range_B_other 7.808 r_dihedral_angle_2_deg 5.702 r_dihedral_angle_1_deg 5.319 r_scangle_other 3.788 r_scbond_it 2.707 r_scbond_other 2.51 r_angle_refined_deg 1.935 r_mcangle_it 1.583 r_mcangle_other 1.583 r_mcbond_it 1.016 r_mcbond_other 1.016 r_angle_other_deg 0.682 r_chiral_restr 0.098 r_bond_refined_d 0.012 r_gen_planes_refined 0.01 r_gen_planes_other 0.002 r_bond_other_d 0.001 r_dihedral_angle_4_deg r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 28197 Nucleic Acid Atoms Solvent Atoms 4490 Heterogen Atoms 334
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing PHENIX model building