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Structure of E.coli Class 2 L-asparaginase EcAIII, wild type (WT EcAIII)
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 2.1 41.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.478 α = 90 b = 75.347 β = 90 c = 147.991 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) 0.97000 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 1.55 75.35 99.5 0.167 0.158 0.997 9.36 12.2 83105
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 1.55 1.64 98 1.39 1.237 0.904 1.62
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 1.65 67.236 68544 814 99.587 0.193 0.1926 0.2348 0.2585 28.294
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] 4.036 -0.969 -3.067
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.418 r_dihedral_angle_4_deg 15.917 r_dihedral_angle_3_deg 12.857 r_dihedral_angle_1_deg 6.848 r_lrange_it 5.274 r_lrange_other 5.191 r_scangle_it 2.538 r_scangle_other 2.538 r_mcangle_it 2.039 r_mcangle_other 2.039
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.418 r_dihedral_angle_4_deg 15.917 r_dihedral_angle_3_deg 12.857 r_dihedral_angle_1_deg 6.848 r_lrange_it 5.274 r_lrange_other 5.191 r_scangle_it 2.538 r_scangle_other 2.538 r_mcangle_it 2.039 r_mcangle_other 2.039 r_angle_refined_deg 1.694 r_scbond_it 1.605 r_scbond_other 1.602 r_angle_other_deg 1.564 r_mcbond_it 1.348 r_mcbond_other 1.346 r_nbd_other 0.211 r_nbd_refined 0.21 r_symmetry_nbd_other 0.182 r_symmetry_nbd_refined 0.174 r_nbtor_refined 0.166 r_symmetry_xyhbond_nbd_refined 0.159 r_xyhbond_nbd_refined 0.141 r_metal_ion_refined 0.112 r_chiral_restr 0.086 r_symmetry_nbtor_other 0.086 r_ncsr_local_group_1 0.081 r_ncsr_local_group_2 0.067 r_bond_refined_d 0.012 r_gen_planes_refined 0.009 r_bond_other_d 0.003 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4209 Nucleic Acid Atoms Solvent Atoms 410 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing