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Structure of E.coli Class 2 L-asparaginase EcAIII, mutant RDM1-38 (R207C, D210S, S211V)
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 30% PEG 4000, 0.2 M MgCl2 in 0.1M Tris-HCl pH 8.5
Crystal Properties Matthews coefficient Solvent content 2.05 40.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.815 α = 90 b = 74.691 β = 90 c = 147.358 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-6000HE 2020-05-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SEALED TUBE Agilent SuperNova 1.54056
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 1.95 21.131 95.3 0.099 0.121 0.991 7 2.7 38942
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 1.95 2 0.361 0.464 0.741 2.1
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 1.95 21.131 38826 1020 94.765 0.249 0.248 0.2531 0.2832 0.293 15.092
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] 2.384 -1.841 -0.543
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.595 r_dihedral_angle_4_deg 15.245 r_dihedral_angle_3_deg 14.753 r_dihedral_angle_1_deg 7.528 r_lrange_it 3.479 r_lrange_other 3.451 r_angle_refined_deg 1.617 r_angle_other_deg 1.38 r_mcangle_other 1.024 r_mcangle_it 1.023
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.595 r_dihedral_angle_4_deg 15.245 r_dihedral_angle_3_deg 14.753 r_dihedral_angle_1_deg 7.528 r_lrange_it 3.479 r_lrange_other 3.451 r_angle_refined_deg 1.617 r_angle_other_deg 1.38 r_mcangle_other 1.024 r_mcangle_it 1.023 r_scangle_it 1.015 r_scangle_other 1.015 r_scbond_it 0.619 r_scbond_other 0.618 r_mcbond_it 0.576 r_mcbond_other 0.575 r_nbd_other 0.303 r_symmetry_nbd_refined 0.268 r_symmetry_xyhbond_nbd_refined 0.25 r_nbd_refined 0.217 r_symmetry_nbd_other 0.187 r_metal_ion_refined 0.178 r_xyhbond_nbd_refined 0.174 r_nbtor_refined 0.16 r_symmetry_nbtor_other 0.084 r_chiral_restr 0.07 r_symmetry_xyhbond_nbd_other 0.043 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_gen_planes_other 0.004 r_bond_other_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4180 Nucleic Acid Atoms Solvent Atoms 170 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement CrysalisPro data reduction Aimless data scaling PHASER phasing