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Structure of E. coli Class 2 L-asparaginase EcAIII, mutant M200W (crystal M200W#1)
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 8.5 293 20-30% PEG4000, 10-15% PEG400, 0.2 M CaCl2 in 100 mM Tris-HCl pH 8.5
Crystal Properties Matthews coefficient Solvent content 2.48 50.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.692 α = 90 b = 70.844 β = 90 c = 149.581 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) 0.97630 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 1.45 74.79 99.6 0.085 0.088 0.999 16.1 13 117826
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 1.45 1.48 1.828 1.907 0.797 1.6 12.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 2ZAL 1.452 74.79 117709 1068 99.644 0.127 0.1268 0.1292 0.1621 0.1648 24.445
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] 1.023 1.528 -2.551
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.392 r_dihedral_angle_4_deg 14.896 r_dihedral_angle_3_deg 11.744 r_dihedral_angle_1_deg 6.273 r_lrange_it 4.879 r_lrange_other 4.54 r_scangle_it 4.206 r_scangle_other 4.205 r_scbond_it 3.493 r_scbond_other 3.493
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.392 r_dihedral_angle_4_deg 14.896 r_dihedral_angle_3_deg 11.744 r_dihedral_angle_1_deg 6.273 r_lrange_it 4.879 r_lrange_other 4.54 r_scangle_it 4.206 r_scangle_other 4.205 r_scbond_it 3.493 r_scbond_other 3.493 r_mcangle_other 2.774 r_mcangle_it 2.765 r_rigid_bond_restr 2.253 r_mcbond_it 2.181 r_mcbond_other 2.165 r_angle_other_deg 1.509 r_angle_refined_deg 1.495 r_symmetry_nbd_refined 0.262 r_nbd_other 0.222 r_nbd_refined 0.216 r_symmetry_xyhbond_nbd_refined 0.177 r_symmetry_metal_ion_refined 0.171 r_symmetry_nbd_other 0.17 r_nbtor_refined 0.159 r_xyhbond_nbd_refined 0.148 r_metal_ion_refined 0.114 r_symmetry_nbtor_other 0.085 r_chiral_restr 0.08 r_bond_refined_d 0.009 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 4267 Nucleic Acid Atoms Solvent Atoms 656 Heterogen Atoms 56
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing