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Structure of E. coli Class 2 L-asparaginase EcAIII, mutant M200T (crystal M200T#o)
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 magnesium chloride in 100mM Tris-HCl pH 8.5
Crystal Properties Matthews coefficient Solvent content 2.09 41.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.852 α = 90 b = 75.886 β = 90 c = 147.762 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) 0.976300 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 1.22 73.89 99.9 0.072 0.075 0.999 16.4 12.7 166404
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 1.22 1.24 98.6 1.696 1.771 0.596 1.6 12.1
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 NONE 2ZAL 1.221 73.89 166293 1018 99.88 0.129 0.1284 0.1283 0.1502 0.1497 16.927
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] 0.664 0.012 -0.676
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.539 r_dihedral_angle_4_deg 15.415 r_dihedral_angle_3_deg 11.726 r_dihedral_angle_1_deg 6.298 r_lrange_it 2.585 r_lrange_other 2.51 r_scangle_it 1.531 r_scangle_other 1.531 r_angle_other_deg 1.47 r_angle_refined_deg 1.295
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.539 r_dihedral_angle_4_deg 15.415 r_dihedral_angle_3_deg 11.726 r_dihedral_angle_1_deg 6.298 r_lrange_it 2.585 r_lrange_other 2.51 r_scangle_it 1.531 r_scangle_other 1.531 r_angle_other_deg 1.47 r_angle_refined_deg 1.295 r_scbond_it 1.226 r_scbond_other 1.224 r_mcangle_it 1.194 r_mcangle_other 1.194 r_mcbond_it 0.886 r_mcbond_other 0.871 r_rigid_bond_restr 0.725 r_nbd_refined 0.21 r_nbd_other 0.21 r_symmetry_nbd_refined 0.2 r_symmetry_nbd_other 0.168 r_nbtor_refined 0.155 r_symmetry_xyhbond_nbd_refined 0.129 r_xyhbond_nbd_refined 0.126 r_metal_ion_refined 0.103 r_symmetry_nbtor_other 0.081 r_chiral_restr 0.064 r_bond_refined_d 0.006 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4257 Nucleic Acid Atoms Solvent Atoms 594 Heterogen Atoms 7
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing