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Crystal structure of potassium-independent L-asparaginase from Phaseolus vulgaris (PvAIII, PvAspG2)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4PV3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 2.0 M ammonium sulfate and 5% v/v 2-propanol
Crystal Properties Matthews coefficient Solvent content 2.64 53.43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 123.764 α = 90 b = 123.645 β = 90.063 c = 187.679 γ = 90
Symmetry Space Group P 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 EIGER X 16M 2022-12-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 0.729310 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 1.879 47.69 98.7 0.083 0.074 0.998 13.43 6.93 451021
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 1.879 1.99 0.813 0.774 0.98 2.1
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 1.879 47.688 450991 6207 98.373 0.183 0.1824 0.193 0.2111 0.2252 30.984
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] 5.505 0.758 5.128 -10.633
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.09 r_dihedral_angle_4_deg 18.364 r_dihedral_angle_3_deg 14.328 r_dihedral_angle_1_deg 6.969 r_lrange_it 4.966 r_lrange_other 4.959 r_scangle_it 3.435 r_scangle_other 3.434 r_mcangle_it 2.37 r_mcangle_other 2.37
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.09 r_dihedral_angle_4_deg 18.364 r_dihedral_angle_3_deg 14.328 r_dihedral_angle_1_deg 6.969 r_lrange_it 4.966 r_lrange_other 4.959 r_scangle_it 3.435 r_scangle_other 3.434 r_mcangle_it 2.37 r_mcangle_other 2.37 r_scbond_it 2.266 r_scbond_other 2.262 r_angle_refined_deg 1.717 r_mcbond_it 1.69 r_mcbond_other 1.69 r_angle_other_deg 1.418 r_nbd_other 0.26 r_symmetry_nbd_refined 0.235 r_symmetry_xyhbond_nbd_refined 0.219 r_nbd_refined 0.21 r_symmetry_nbd_other 0.182 r_xyhbond_nbd_refined 0.16 r_xyhbond_nbd_other 0.16 r_nbtor_refined 0.153 r_metal_ion_refined 0.124 r_symmetry_xyhbond_nbd_other 0.102 r_chiral_restr 0.09 r_symmetry_nbtor_other 0.085 r_bond_refined_d 0.011 r_gen_planes_refined 0.009 r_gen_planes_other 0.004 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 34011 Nucleic Acid Atoms Solvent Atoms 2466 Heterogen Atoms 229
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing