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Structure of E.coli Class 2 L-asparaginase EcAIII, mutant RDM1-12 (G206C, R207T, D210A, S211A)
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 6000, 0.2 M MgCl2 in 0.1M Tris-HCl pH 8.5
Crystal Properties Matthews coefficient Solvent content 2.16 43.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.623 α = 90 b = 75.052 β = 90 c = 149.137 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 2020-07-16 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 1.6 19.05 90.7 0.056 0.07 0.995 9.8 2.3 69731
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 1.6 1.63 86.8 0.22 0.293 0.883 1.8
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 1.6 19.05 69700 1039 90.157 0.174 0.1737 0.1846 0.2109 0.2217 16.778
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] -0.082 0.022 0.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.119 r_dihedral_angle_4_deg 14.511 r_dihedral_angle_3_deg 12.632 r_lrange_it 7.31 r_lrange_other 7.278 r_dihedral_angle_1_deg 6.82 r_scangle_it 5.7 r_scangle_other 5.699 r_scbond_it 4.46 r_scbond_other 4.459
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.119 r_dihedral_angle_4_deg 14.511 r_dihedral_angle_3_deg 12.632 r_lrange_it 7.31 r_lrange_other 7.278 r_dihedral_angle_1_deg 6.82 r_scangle_it 5.7 r_scangle_other 5.699 r_scbond_it 4.46 r_scbond_other 4.459 r_mcangle_it 2.322 r_mcangle_other 2.322 r_mcbond_it 1.871 r_mcbond_other 1.863 r_angle_refined_deg 1.672 r_angle_other_deg 1.65 r_symmetry_nbd_refined 0.245 r_nbd_other 0.217 r_nbd_refined 0.212 r_symmetry_xyhbond_nbd_refined 0.209 r_symmetry_nbd_other 0.182 r_xyhbond_nbd_refined 0.157 r_nbtor_refined 0.153 r_metal_ion_refined 0.121 r_chiral_restr 0.083 r_symmetry_nbtor_other 0.07 r_bond_other_d 0.015 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 r_gen_planes_other 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4198 Nucleic Acid Atoms Solvent Atoms 597 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement CrysalisPro data reduction Aimless data scaling PHASER phasing