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L-asparaginase II (EcA2-K12)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3ECA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.1 298 0.2 M Ammonium acetate, 20% w/v Polyethylene glycol 3,350.
Crystal Properties Matthews coefficient Solvent content 1.98 38.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.746 α = 90 b = 123.051 β = 108.98 c = 79.071 γ = 90
Symmetry Space Group P 1 21 1
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 2M 2023-12-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON LNLS SIRIUS BEAMLINE MANACA 0.97718 LNLS SIRIUS MANACA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.35 47.51 99.93 0.843 14.57 20 44971
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.35 47.51 0.843
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.35 47.509 44971 2249 99.927 0.177 0.1728 0.2494 0.2397 22.873
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] -0.014 -0.003 0.005 0.008
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.21 r_dihedral_angle_3_deg 15.132 r_dihedral_angle_2_deg 9.768 r_dihedral_angle_1_deg 7.373 r_lrange_it 6.924 r_lrange_other 6.912 r_scangle_it 4.255 r_scangle_other 4.254 r_mcangle_it 3.79 r_mcangle_other 3.79
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.21 r_dihedral_angle_3_deg 15.132 r_dihedral_angle_2_deg 9.768 r_dihedral_angle_1_deg 7.373 r_lrange_it 6.924 r_lrange_other 6.912 r_scangle_it 4.255 r_scangle_other 4.254 r_mcangle_it 3.79 r_mcangle_other 3.79 r_scbond_it 2.583 r_scbond_other 2.583 r_mcbond_it 2.329 r_mcbond_other 2.328 r_angle_refined_deg 1.723 r_angle_other_deg 0.583 r_symmetry_xyhbond_nbd_refined 0.273 r_symmetry_nbd_refined 0.244 r_nbd_refined 0.214 r_symmetry_nbd_other 0.207 r_nbd_other 0.204 r_nbtor_refined 0.174 r_xyhbond_nbd_refined 0.164 r_symmetry_xyhbond_nbd_other 0.114 r_symmetry_nbtor_other 0.084 r_chiral_restr 0.08 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9724 Nucleic Acid Atoms Solvent Atoms 462 Heterogen Atoms 61
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction autoPROC data scaling