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Crystal structure of Rhizobium etli constitutive L-asparaginase ReAIV (tetragonal form R4tP)
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, SITTING DROP 293 0.2 M ammonium formate, 20 % (w/v) PEG 3350, and 0.2% lauryldimethylamine oxide (LDAO)
Crystal Properties Matthews coefficient Solvent content 3.19 61.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 125.344 α = 90 b = 125.344 β = 90 c = 115.227 γ = 90
Symmetry Space Group P 42 21 2
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 EIGER2 S 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) 0.9700 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 2.5 88.63 99.9 0.176 0.187 0.996 11.41 8.82 32235 44.99
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 2.5 2.65 1.016 1.079 0.739 2.16
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.503 88.63 32215 1000 99.904 0.173 0.1721 0.2165 0.1927 40.493
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] 1.276 1.276 -2.551
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.79 r_dihedral_angle_4_deg 18.714 r_dihedral_angle_3_deg 14.916 r_dihedral_angle_1_deg 6.694 r_lrange_it 4.936 r_lrange_other 4.927 r_scangle_it 3.962 r_scangle_other 3.962 r_mcangle_it 2.72 r_mcangle_other 2.72
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.79 r_dihedral_angle_4_deg 18.714 r_dihedral_angle_3_deg 14.916 r_dihedral_angle_1_deg 6.694 r_lrange_it 4.936 r_lrange_other 4.927 r_scangle_it 3.962 r_scangle_other 3.962 r_mcangle_it 2.72 r_mcangle_other 2.72 r_scbond_it 2.474 r_scbond_other 2.474 r_mcbond_it 1.813 r_mcbond_other 1.802 r_angle_refined_deg 1.517 r_angle_other_deg 1.344 r_nbd_other 0.302 r_symmetry_xyhbond_nbd_refined 0.231 r_nbd_refined 0.188 r_symmetry_nbd_other 0.188 r_symmetry_nbd_refined 0.163 r_nbtor_refined 0.153 r_xyhbond_nbd_refined 0.122 r_symmetry_nbtor_other 0.082 r_chiral_restr 0.075 r_ncsr_local_group_1 0.065 r_symmetry_xyhbond_nbd_other 0.011 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_xyhbond_nbd_other 0.006 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4930 Nucleic Acid Atoms Solvent Atoms 160 Heterogen Atoms 8
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing