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Crystal structure of Bacillus subtilis 168 L-asparaginase II with antileukemic activity
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 285.15 PEG 400 25 %, HEPES 0.1 M, NaCl 0.1 M
Crystal Properties Matthews coefficient Solvent content 2.06 40.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 102.234 α = 90 b = 104.486 β = 90 c = 123.055 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 2M 2022-12-03 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 1.3 48.135 100 0.99 1.5 1.9 321574
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 1.3 1.32 100 0.54 1.2 2
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.3 48.13 305395 16178 99.99 0.13695 0.13552 0.1387 0.16433 0.1666 RANDOM 16.358
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] 0.45 -0.45 0.01
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 14.593 r_long_range_B_other 13.409 r_dihedral_angle_3_deg 12.803 r_scangle_other 10.797 r_scbond_it 7.605 r_scbond_other 7.603 r_mcangle_it 6.933 r_mcangle_other 6.932 r_dihedral_angle_2_deg 6.308 r_dihedral_angle_1_deg 6.296
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 14.593 r_long_range_B_other 13.409 r_dihedral_angle_3_deg 12.803 r_scangle_other 10.797 r_scbond_it 7.605 r_scbond_other 7.603 r_mcangle_it 6.933 r_mcangle_other 6.932 r_dihedral_angle_2_deg 6.308 r_dihedral_angle_1_deg 6.296 r_mcbond_it 4.902 r_mcbond_other 4.902 r_rigid_bond_restr 4.06 r_angle_refined_deg 1.678 r_angle_other_deg 0.589 r_chiral_restr 0.094 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 r_gen_planes_other 0.002 r_bond_other_d 0.001 r_dihedral_angle_4_deg r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9427 Nucleic Acid Atoms Solvent Atoms 1124 Heterogen Atoms 8
Software Software Software Name Purpose REFMAC refinement XDS data reduction pointless data scaling MOLREP phasing