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Crystal structure of Rhizobium etli constitutive L-asparaginase ReAIV (orthorombic form R4oP-2)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7OS5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 0.1 M Tris pH 8.5, 0.2 M MgCl2, 17.5% PEG 8000, 0.3% dodecyl-beta-D-maltoside (DDM)
Crystal Properties Matthews coefficient Solvent content 2.18 43.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.101 α = 90 b = 89.749 β = 90 c = 169.197 γ = 90
Symmetry Space Group P 21 21 21
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 2022-05-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 0.9763 PETRA III, EMBL c/o DESY P13 (MX1)
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 2 84.6 99.7 0.135 0.148 0.998 10.22 5.94 86068 34.76
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 2 2.12 1.115 1.22 0.681 1.45 6.11
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2 84.599 86052 1000 99.711 0.177 0.1767 0.19 0.2343 0.2436 31.057
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] -2.121 4.47 -2.349
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.233 r_dihedral_angle_other_3_deg 23.673 r_dihedral_angle_4_deg 15.999 r_dihedral_angle_3_deg 13.74 r_dihedral_angle_1_deg 6.991 r_lrange_it 4.909 r_lrange_other 4.907 r_scangle_it 3.333 r_scangle_other 3.332 r_mcangle_it 2.415
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.233 r_dihedral_angle_other_3_deg 23.673 r_dihedral_angle_4_deg 15.999 r_dihedral_angle_3_deg 13.74 r_dihedral_angle_1_deg 6.991 r_lrange_it 4.909 r_lrange_other 4.907 r_scangle_it 3.333 r_scangle_other 3.332 r_mcangle_it 2.415 r_mcangle_other 2.415 r_scbond_it 2.152 r_scbond_other 2.152 r_angle_refined_deg 1.731 r_mcbond_it 1.674 r_mcbond_other 1.674 r_angle_other_deg 1.48 r_symmetry_xyhbond_nbd_refined 0.212 r_nbd_refined 0.209 r_symmetry_nbd_refined 0.197 r_symmetry_nbd_other 0.189 r_xyhbond_nbd_refined 0.185 r_nbd_other 0.173 r_nbtor_refined 0.162 r_xyhbond_nbd_other 0.103 r_metal_ion_refined 0.102 r_symmetry_metal_ion_refined 0.094 r_symmetry_nbtor_other 0.083 r_chiral_restr 0.078 r_symmetry_xyhbond_nbd_other 0.041 r_bond_refined_d 0.011 r_gen_planes_refined 0.008 r_bond_other_d 0.003 r_gen_planes_other 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9878 Nucleic Acid Atoms Solvent Atoms 882 Heterogen Atoms 31
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing