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Crystal structure of L-asparaginase from Thermococcus Sibiricus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5OT0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 292 0.2 M Ammonium acetate, 20% w/v Polyethylene glycol 3,350
Crystal Properties Matthews coefficient Solvent content 2.33 47.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.193 α = 90 b = 57.791 β = 90 c = 131.158 γ = 90
Symmetry Space Group P 2 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 RIGAKU HyPix-6000HE 2022-12-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.54184
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim 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 1.9 24.11 95.3 0.08 0.084 0.025 0.999 21.7 11.2 26391
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 1.94 92.8 0.308 0.321 0.088 0.975 13.2
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 (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 5OT0 1.9 24.11 25057 1293 94.51 0.16944 0.16709 0.1765 0.21445 0.2221 RANDOM 18.136
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] -0.98 0.65 0.34
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.167 r_dihedral_angle_4_deg 17.473 r_dihedral_angle_3_deg 14.686 r_dihedral_angle_1_deg 7.239 r_long_range_B_refined 4.832 r_long_range_B_other 4.591 r_scangle_other 3.331 r_mcangle_it 2.479 r_mcangle_other 2.479 r_scbond_it 2.232
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.167 r_dihedral_angle_4_deg 17.473 r_dihedral_angle_3_deg 14.686 r_dihedral_angle_1_deg 7.239 r_long_range_B_refined 4.832 r_long_range_B_other 4.591 r_scangle_other 3.331 r_mcangle_it 2.479 r_mcangle_other 2.479 r_scbond_it 2.232 r_scbond_other 2.232 r_angle_refined_deg 1.799 r_mcbond_it 1.647 r_mcbond_other 1.643 r_angle_other_deg 1.356 r_chiral_restr 0.096 r_bond_refined_d 0.011 r_gen_planes_refined 0.009 r_gen_planes_other 0.004 r_bond_other_d 0.003 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2518 Nucleic Acid Atoms Solvent Atoms 251 Heterogen Atoms 10
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction CrysalisPro data reduction MOLREP phasing PDB_EXTRACT data extraction