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Structure of E. coli Class 2 L-asparaginase EcAIII, mutant M200L (acyl-enzyme intermediate)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2ZAL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 20 PEG4000, 10% PEG400, 0.2 M MgCl2 in 100 mM Tris-HCl pH 8.5
Crystal Properties Matthews coefficient Solvent content 2.04 39.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.71 α = 90 b = 74.851 β = 90 c = 146.595 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 RIGAKU HyPix-3000 2022-10-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SEALED TUBE RIGAKU PhotonJet-S 1.54184
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 1.9 19.3 97.6 0.148 0.177 0.949 18 3.1 42775
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 1.9 1.9 97.8 0.283 0.344 0.865 3.2
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 1.9 19.3 42735 1022 97.114 0.233 0.2319 0.2347 0.2752 0.278 21.496
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] -1.906 -0.017 1.924
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.11 r_dihedral_angle_4_deg 20.23 r_dihedral_angle_3_deg 14.531 r_dihedral_angle_1_deg 7.492 r_lrange_it 3.221 r_lrange_other 3.14 r_mcangle_it 1.617 r_mcangle_other 1.617 r_angle_refined_deg 1.553 r_scangle_it 1.55
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.11 r_dihedral_angle_4_deg 20.23 r_dihedral_angle_3_deg 14.531 r_dihedral_angle_1_deg 7.492 r_lrange_it 3.221 r_lrange_other 3.14 r_mcangle_it 1.617 r_mcangle_other 1.617 r_angle_refined_deg 1.553 r_scangle_it 1.55 r_scangle_other 1.55 r_angle_other_deg 1.38 r_mcbond_it 0.979 r_mcbond_other 0.978 r_scbond_it 0.938 r_scbond_other 0.937 r_metal_ion_refined 0.221 r_nbd_other 0.216 r_symmetry_xyhbond_nbd_refined 0.21 r_nbd_refined 0.201 r_symmetry_nbd_refined 0.196 r_symmetry_nbd_other 0.194 r_xyhbond_nbd_refined 0.164 r_nbtor_refined 0.159 r_ncsr_local_group_1 0.099 r_ncsr_local_group_2 0.098 r_symmetry_nbtor_other 0.085 r_chiral_restr 0.071 r_symmetry_xyhbond_nbd_other 0.054 r_bond_refined_d 0.01 r_gen_planes_refined 0.007 r_bond_other_d 0.003 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4214 Nucleic Acid Atoms Solvent Atoms 185 Heterogen Atoms 5
Software Software Software Name Purpose REFMAC refinement CrysalisPro data reduction Aimless data scaling PHASER phasing