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Structure of E.coli Class 2 L-asparaginase EcAIII, mutant RDM1-8 (G206Y, R207Q, D210P, S211T)
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 4000; 15% PEG 400; 0,2 M MgCl2 in 0.1M Tris-HCl pH 8.5
Crystal Properties Matthews coefficient Solvent content 2.06 40.43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.005 α = 90 b = 74.885 β = 90 c = 147.835 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 2020-07-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SEALED TUBE agilent 1.5406
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 1.8 19.161 93.6 0.076 0.092 0.996 8 2.6 48975
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 1.8 1.84 0.519 0.631 0.692 1.6
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 1.8 19.161 48924 1001 93.436 0.196 0.1955 0.2025 0.2365 0.2368 17.964
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] 0.364 0.11 -0.474
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.215 r_dihedral_angle_4_deg 14.373 r_dihedral_angle_3_deg 13.787 r_dihedral_angle_1_deg 7.031 r_lrange_it 4.294 r_lrange_other 4.272 r_scangle_it 2.171 r_scangle_other 2.17 r_mcangle_it 1.864 r_mcangle_other 1.863
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.215 r_dihedral_angle_4_deg 14.373 r_dihedral_angle_3_deg 13.787 r_dihedral_angle_1_deg 7.031 r_lrange_it 4.294 r_lrange_other 4.272 r_scangle_it 2.171 r_scangle_other 2.17 r_mcangle_it 1.864 r_mcangle_other 1.863 r_angle_refined_deg 1.609 r_angle_other_deg 1.473 r_scbond_it 1.326 r_scbond_other 1.321 r_mcbond_it 1.07 r_mcbond_other 1.069 r_symmetry_nbd_refined 0.297 r_nbd_other 0.272 r_symmetry_xyhbond_nbd_refined 0.233 r_nbd_refined 0.215 r_xyhbond_nbd_refined 0.193 r_symmetry_nbd_other 0.186 r_nbtor_refined 0.162 r_metal_ion_refined 0.158 r_ncsr_local_group_1 0.093 r_symmetry_nbtor_other 0.085 r_chiral_restr 0.072 r_symmetry_xyhbond_nbd_other 0.058 r_ncsr_local_group_2 0.057 r_bond_refined_d 0.011 r_gen_planes_refined 0.008 r_bond_other_d 0.004 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4218 Nucleic Acid Atoms Solvent Atoms 412 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement CrysalisPro data reduction Aimless data scaling PHASER phasing