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Structure of E.coli Class 2 L-asparaginase EcAIII, mutant RDM1-24 (R207A, D210S, 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 6K; 15% PEG 400; 0.2M MgCl2 in 0.1 Tris-HCl pH 8.5
Crystal Properties Matthews coefficient Solvent content 2.06 40.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.258 α = 90 b = 74.141 β = 90 c = 147.466 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 PILATUS 6M 2021-06-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 0.77490 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 1.85 52.335 98.4 0.119 0.118 0.999 15.16 13.1 48066
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 1.85 1.95 97.7 2.141 1.852 0.789 1.75 12.4
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 1.85 52.335 47941 1031 99.948 0.199 0.1984 0.2105 0.2385 0.2395 32.827
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] 4.174 0.061 -4.235
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.211 r_dihedral_angle_4_deg 14.485 r_dihedral_angle_3_deg 13.892 r_dihedral_angle_1_deg 6.889 r_lrange_it 5.559 r_lrange_other 5.542 r_scangle_it 3.808 r_scangle_other 3.806 r_mcangle_other 2.633 r_mcangle_it 2.631
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.211 r_dihedral_angle_4_deg 14.485 r_dihedral_angle_3_deg 13.892 r_dihedral_angle_1_deg 6.889 r_lrange_it 5.559 r_lrange_other 5.542 r_scangle_it 3.808 r_scangle_other 3.806 r_mcangle_other 2.633 r_mcangle_it 2.631 r_scbond_it 2.439 r_scbond_other 2.434 r_mcbond_it 1.779 r_mcbond_other 1.767 r_angle_refined_deg 1.568 r_angle_other_deg 1.484 r_nbd_other 0.236 r_symmetry_xyhbond_nbd_refined 0.218 r_nbd_refined 0.208 r_symmetry_nbd_refined 0.196 r_symmetry_nbd_other 0.178 r_nbtor_refined 0.163 r_xyhbond_nbd_refined 0.147 r_metal_ion_refined 0.104 r_symmetry_nbtor_other 0.088 r_chiral_restr 0.075 r_ncsr_local_group_1 0.062 r_ncsr_local_group_2 0.051 r_bond_refined_d 0.011 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4063 Nucleic Acid Atoms Solvent Atoms 208 Heterogen Atoms 5
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing