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Crystal structure of Rhizobium etli constitutive L-asparaginase ReAIV (monoclinic form R4mC-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 0.2 M ammonium formate, 20 % (w/v) PEG 3350, and 0.2% lauryldimethylamine oxide (LDAO)
Crystal Properties Matthews coefficient Solvent content 2.27 45.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.245 α = 90 b = 85.298 β = 109.178 c = 82.946 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 PIXEL DECTRIS EIGER X 16M 2021-11-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 0.9770 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 1.5 78.34 99.1 0.088 0.107 0.994 6.6 2.99 100056 26.72
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 1.5 1.59 0.849 1.044 0.517 1.12
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 1.501 78.34 100046 1000 99.172 0.254 0.2533 0.2629 0.3024 0.3086 22.51
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] 0.903 -0.16 1.462 -1.815
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.885 r_dihedral_angle_4_deg 14 r_dihedral_angle_3_deg 13.754 r_dihedral_angle_1_deg 6.526 r_lrange_it 3.913 r_lrange_other 3.813 r_scangle_it 2.698 r_scangle_other 2.697 r_mcangle_other 2.142 r_mcangle_it 2.139
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.885 r_dihedral_angle_4_deg 14 r_dihedral_angle_3_deg 13.754 r_dihedral_angle_1_deg 6.526 r_lrange_it 3.913 r_lrange_other 3.813 r_scangle_it 2.698 r_scangle_other 2.697 r_mcangle_other 2.142 r_mcangle_it 2.139 r_scbond_it 1.821 r_scbond_other 1.821 r_angle_refined_deg 1.479 r_mcbond_it 1.46 r_mcbond_other 1.452 r_angle_other_deg 1.319 r_metal_ion_refined 0.21 r_symmetry_xyhbond_nbd_refined 0.196 r_nbd_refined 0.195 r_xyhbond_nbd_refined 0.192 r_symmetry_nbd_other 0.182 r_nbd_other 0.181 r_symmetry_nbd_refined 0.172 r_nbtor_refined 0.153 r_symmetry_xyhbond_nbd_other 0.12 r_symmetry_nbtor_other 0.078 r_chiral_restr 0.07 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4930 Nucleic Acid Atoms Solvent Atoms 376 Heterogen Atoms 7
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing