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Crystal structure of mutant R43D/C273S of L-Asparaginase I from Yersinia pestis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3NTX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 8 293 0.2 M Ammonium chloride, 0.1 M Tris, pH 8.0, 20% (w/v) PEG 6000
Crystal Properties Matthews coefficient Solvent content 2.55 51.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.979 α = 90 b = 162.98 β = 110.39 c = 73.26 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 EIGER X 16M 2020-07-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.0 APS 22-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.8 50 98.5 0.056 0.032 0.998 21.8 3.9 133825
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.83 95.6 0.535 0.313 0.78 1.8 3.7
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 3NTX 1.8 41.12 128764 1882 96.09 0.1673 0.1669 0.1802 0.1963 0.208 RANDOM 37.483
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] 0.42 -0.09 -0.01 -0.27
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.561 r_dihedral_angle_4_deg 21.853 r_dihedral_angle_3_deg 14.072 r_dihedral_angle_1_deg 7.338 r_angle_refined_deg 1.996 r_angle_other_deg 1.51 r_chiral_restr 0.102 r_bond_refined_d 0.016 r_gen_planes_refined 0.013 r_gen_planes_other 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.561 r_dihedral_angle_4_deg 21.853 r_dihedral_angle_3_deg 14.072 r_dihedral_angle_1_deg 7.338 r_angle_refined_deg 1.996 r_angle_other_deg 1.51 r_chiral_restr 0.102 r_bond_refined_d 0.016 r_gen_planes_refined 0.013 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9534 Nucleic Acid Atoms Solvent Atoms 1021 Heterogen Atoms 52
Software Software Software Name Purpose HKL-3000 data reduction HKL-3000 data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction