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Complex of double mutant (T89V,K162T) of E. coli L-asparaginase II with L-Asp
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3ECA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.2 293 Crystals grown at 0.17 M sodium citrate (pH 6) and 17-18% (w/v) PEG3350. Soaked for 1-2 minutes (empirically determined for each crystal) in equivalent solution with 0.025% (w/v) glutaraldehyde. Finally transferred and soaked for 10-20 sec in solution containing 40% (w/v) PEG3350, 5 mM L-L-Asp, and 0.17 M sodium citrate (pH 6.2)
Crystal Properties Matthews coefficient Solvent content 2.1 41.43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 151.616 α = 90 b = 62.43 β = 118.09 c = 143.066 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 EIGER X 4M 2018-05-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 40 99.1 0.06 0.072 0.039 10.7 3.2 79279
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 2 2.03 98.3 0.526 0.639 0.358 0.717 2.9
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 3eca 2 26 75132 4004 98.94 0.1454 0.1424 0.1546 0.2037 0.2098 RANDOM 30.012
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] 0.12 0.14 -0.42 0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.545 r_dihedral_angle_4_deg 17.131 r_dihedral_angle_3_deg 14.778 r_dihedral_angle_1_deg 6.545 r_angle_refined_deg 1.922 r_angle_other_deg 1.087 r_chiral_restr 0.12 r_bond_refined_d 0.02 r_gen_planes_refined 0.01 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.545 r_dihedral_angle_4_deg 17.131 r_dihedral_angle_3_deg 14.778 r_dihedral_angle_1_deg 6.545 r_angle_refined_deg 1.922 r_angle_other_deg 1.087 r_chiral_restr 0.12 r_bond_refined_d 0.02 r_gen_planes_refined 0.01 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9295 Nucleic Acid Atoms Solvent Atoms 1018 Heterogen Atoms 72
Software Software Software Name Purpose HKL-2000 data reduction HKL-2000 data scaling REFMAC refinement PDB_EXTRACT data extraction PHASER phasing