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L-asparaginase II (EcA2-4M)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1NNS
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 2.13 42.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.083 α = 90 b = 133.902 β = 109.461 c = 63.123 γ = 90
Symmetry Space Group C 1 2 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 2.7 44.48 99.79 0.804 16.302 20 15937
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 2.7 2.8 0.804
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-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.7 44.48 15937 797 99.787 0.243 0.2408 0.2442 0.2751 0.2751 34.652
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] 0.049 0.051 -0.062 -0.018
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 18.003 r_dihedral_angle_6_deg 14.948 r_dihedral_angle_2_deg 8.493 r_dihedral_angle_1_deg 7.851 r_lrange_it 7.707 r_lrange_other 7.703 r_scangle_it 5.36 r_scangle_other 5.359 r_mcangle_it 5.273 r_mcangle_other 5.273
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 18.003 r_dihedral_angle_6_deg 14.948 r_dihedral_angle_2_deg 8.493 r_dihedral_angle_1_deg 7.851 r_lrange_it 7.707 r_lrange_other 7.703 r_scangle_it 5.36 r_scangle_other 5.359 r_mcangle_it 5.273 r_mcangle_other 5.273 r_scbond_it 3.431 r_scbond_other 3.43 r_mcbond_it 3.368 r_mcbond_other 3.367 r_angle_refined_deg 1.896 r_angle_other_deg 0.641 r_nbd_refined 0.231 r_symmetry_nbd_other 0.214 r_nbd_other 0.199 r_symmetry_xyhbond_nbd_refined 0.194 r_xyhbond_nbd_refined 0.185 r_nbtor_refined 0.182 r_symmetry_nbd_refined 0.174 r_symmetry_xyhbond_nbd_other 0.111 r_chiral_restr 0.086 r_symmetry_nbtor_other 0.086 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4862 Nucleic Acid Atoms Solvent Atoms 65 Heterogen Atoms 18
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction autoPROC data scaling