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Complex of mutant (K162M) 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 5.6 293 0.1 M sodium acetate, pH 5.6, 5 mM L-Asp, and 18-20% (w/v) PEG3350
Crystal Properties Matthews coefficient Solvent content 2.06 40.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 151.017 α = 90 b = 62.287 β = 117.54 c = 140.723 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 Multilayer X-ray mirrors VariMax HF 2018-07-17 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 1.8 40 92.3 0.073 0.088 0.048 11.5 3 99158
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 1.8 1.83 61.5 0.324 0.413 0.252 0.749 2.2
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 3eca 1.8 24.95 93692 4755 91.1 0.1866 0.1861 0.2129 0.196 0.2432 RANDOM 25.808
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] -0.75 -1.43 -1.71 2.46
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.362 r_dihedral_angle_4_deg 15.156 r_dihedral_angle_3_deg 14.775 r_dihedral_angle_1_deg 6.778 r_angle_refined_deg 1.96 r_angle_other_deg 1.129 r_chiral_restr 0.119 r_bond_refined_d 0.018 r_gen_planes_refined 0.01 r_bond_other_d 0.003
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.362 r_dihedral_angle_4_deg 15.156 r_dihedral_angle_3_deg 14.775 r_dihedral_angle_1_deg 6.778 r_angle_refined_deg 1.96 r_angle_other_deg 1.129 r_chiral_restr 0.119 r_bond_refined_d 0.018 r_gen_planes_refined 0.01 r_bond_other_d 0.003 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9581 Nucleic Acid Atoms Solvent Atoms 1250 Heterogen Atoms 36
Software Software Software Name Purpose HKL-2000 data reduction HKL-2000 data scaling REFMAC refinement PDB_EXTRACT data extraction PHASER phasing