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Structure of E. coli Class 2 L-asparaginase EcAIII, mutant M200W (crystal M200W#2)
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%PEG400,0.2M MgCl2 in 100 mM Tris-HCl pH 8.5
Crystal Properties Matthews coefficient Solvent content 2.08 40.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.974 α = 90 b = 74.475 β = 90 c = 146.787 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 CCD AGILENT ATLAS CCD 2022-10-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SEALED TUBE Agilent SuperNova 1.5418
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 1.7 73.4 99.1 0.082 0.094 0.995 9.9 4 61686
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 1.7 1.73 97.8 0.378 0.455 0.749 2.5 3.1
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 1.7 73.4 61581 1056 98.781 0.194 0.1933 0.2024 0.2284 0.2329 11.731
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] -0.327 0.46 -0.133
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.424 r_dihedral_angle_4_deg 16.481 r_dihedral_angle_3_deg 13.783 r_dihedral_angle_1_deg 6.953 r_lrange_it 3.083 r_lrange_other 2.954 r_angle_refined_deg 1.598 r_scangle_it 1.561 r_scangle_other 1.561 r_angle_other_deg 1.531
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.424 r_dihedral_angle_4_deg 16.481 r_dihedral_angle_3_deg 13.783 r_dihedral_angle_1_deg 6.953 r_lrange_it 3.083 r_lrange_other 2.954 r_angle_refined_deg 1.598 r_scangle_it 1.561 r_scangle_other 1.561 r_angle_other_deg 1.531 r_mcangle_it 1.303 r_mcangle_other 1.303 r_scbond_it 0.946 r_scbond_other 0.946 r_mcbond_it 0.737 r_mcbond_other 0.737 r_nbd_other 0.277 r_metal_ion_refined 0.258 r_nbd_refined 0.215 r_symmetry_xyhbond_nbd_refined 0.214 r_symmetry_nbd_refined 0.198 r_symmetry_nbd_other 0.188 r_nbtor_refined 0.164 r_xyhbond_nbd_refined 0.157 r_symmetry_nbtor_other 0.083 r_chiral_restr 0.074 r_bond_refined_d 0.011 r_gen_planes_refined 0.008 r_bond_other_d 0.003 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4253 Nucleic Acid Atoms Solvent Atoms 266 Heterogen Atoms 6
Software Software Software Name Purpose REFMAC refinement CrysalisPro data reduction Aimless data scaling PHASER phasing