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Structure of E.coli Class 2 L-asparaginase EcAIII, mutant RDM1-3 (G206H, R207T, D210P, S211Q)
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% PEG 6000, 0.2 M MgCl2 in 0.1M Tris-HCl pH 8.5
Crystal Properties Matthews coefficient Solvent content 2.14 42.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.353 α = 90 b = 75.039 β = 90 c = 149.032 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 2020-07-14 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 2.55 20.36 92.7 0.119 0.143 0.983 7.2 2.8 17974
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 2.55 2.66 95.3 0.676 0.83 0.604 2.1 2.5
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2ZAL 2.55 20.358 17932 1010 92.044 0.205 0.2023 0.2483 0.2189 33.407
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] 0.204 1.543 -1.747
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.155 r_dihedral_angle_4_deg 17.894 r_dihedral_angle_3_deg 15.067 r_dihedral_angle_1_deg 7.093 r_lrange_it 5.949 r_lrange_other 5.925 r_mcangle_it 2.611 r_mcangle_other 2.61 r_scangle_it 2.374 r_scangle_other 2.373
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.155 r_dihedral_angle_4_deg 17.894 r_dihedral_angle_3_deg 15.067 r_dihedral_angle_1_deg 7.093 r_lrange_it 5.949 r_lrange_other 5.925 r_mcangle_it 2.611 r_mcangle_other 2.61 r_scangle_it 2.374 r_scangle_other 2.373 r_angle_refined_deg 1.585 r_mcbond_it 1.468 r_mcbond_other 1.467 r_angle_other_deg 1.39 r_scbond_it 1.365 r_scbond_other 1.363 r_symmetry_xyhbond_nbd_refined 0.399 r_nbd_other 0.326 r_symmetry_nbd_refined 0.325 r_nbd_refined 0.205 r_symmetry_nbd_other 0.197 r_metal_ion_refined 0.187 r_nbtor_refined 0.157 r_xyhbond_nbd_refined 0.152 r_ncsr_local_group_1 0.133 r_ncsr_local_group_2 0.126 r_symmetry_nbtor_other 0.08 r_chiral_restr 0.065 r_symmetry_xyhbond_nbd_other 0.044 r_bond_refined_d 0.009 r_bond_other_d 0.007 r_gen_planes_refined 0.006 r_gen_planes_other 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4022 Nucleic Acid Atoms Solvent Atoms 142 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement CrysalisPro data reduction Aimless data scaling PHASER phasing