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Structure of E.coli Class 2 L-asparaginase EcAIII, mutant M200I
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 100mM Tris-HCl pH 8.5
Crystal Properties Matthews coefficient Solvent content 2.41 48.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.923 α = 90 b = 77.671 β = 90 c = 148.28 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 2021-07-05 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 2.1 17.21 97.9 0.142 0.169 0.983 5.2 2.9 35616
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 2.1 2.16 99 0.663 0.838 0.514 2.7 2.3
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 2.1 17.209 35579 1064 97.453 0.184 0.1823 0.1918 0.2315 0.242 18.42
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] 1.123 -0.273 -0.85
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.494 r_dihedral_angle_4_deg 18.831 r_dihedral_angle_3_deg 13.569 r_dihedral_angle_1_deg 6.896 r_lrange_it 4.172 r_lrange_other 4.144 r_scangle_it 2.896 r_scangle_other 2.895 r_mcangle_it 1.984 r_mcangle_other 1.984
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.494 r_dihedral_angle_4_deg 18.831 r_dihedral_angle_3_deg 13.569 r_dihedral_angle_1_deg 6.896 r_lrange_it 4.172 r_lrange_other 4.144 r_scangle_it 2.896 r_scangle_other 2.895 r_mcangle_it 1.984 r_mcangle_other 1.984 r_scbond_it 1.811 r_scbond_other 1.81 r_angle_refined_deg 1.523 r_angle_other_deg 1.354 r_mcbond_it 1.254 r_mcbond_other 1.253 r_nbd_other 0.225 r_nbd_refined 0.209 r_symmetry_nbd_other 0.177 r_xyhbond_nbd_refined 0.157 r_nbtor_refined 0.156 r_symmetry_nbd_refined 0.139 r_symmetry_xyhbond_nbd_refined 0.126 r_symmetry_nbtor_other 0.082 r_metal_ion_refined 0.071 r_chiral_restr 0.068 r_symmetry_xyhbond_nbd_other 0.058 r_bond_refined_d 0.009 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4244 Nucleic Acid Atoms Solvent Atoms 234 Heterogen Atoms 15
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing