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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 5.2 293 0.1 M sodium acetate, pH 5.2, 5 mM L-Asp, and 18-20% (w/v) PEG3350
Crystal Properties Matthews coefficient Solvent content 2.02 39.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.53 α = 90 b = 123.967 β = 96.8 c = 76.302 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 4M Multilayer X-ray mirrors VariMax HF 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 1.78 40 94.3 0.024 0.029 0.017 21.3 2.8 102698
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 1.78 1.81 62.3 0.309 0.398 0.246 0.829 1.9
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 1.78 24.61 98474 2442 93.02 0.1374 0.136 0.1483 0.1928 0.2013 RANDOM 29.504
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] 0.02 0.09 -0.06 0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.237 r_dihedral_angle_4_deg 17.901 r_dihedral_angle_3_deg 15.121 r_dihedral_angle_1_deg 7.222 r_angle_refined_deg 2.222 r_angle_other_deg 2.107 r_chiral_restr 0.115 r_bond_refined_d 0.019 r_gen_planes_refined 0.014 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.237 r_dihedral_angle_4_deg 17.901 r_dihedral_angle_3_deg 15.121 r_dihedral_angle_1_deg 7.222 r_angle_refined_deg 2.222 r_angle_other_deg 2.107 r_chiral_restr 0.115 r_bond_refined_d 0.019 r_gen_planes_refined 0.014 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9653 Nucleic Acid Atoms Solvent Atoms 1484 Heterogen Atoms 18
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PDB_EXTRACT data extraction PHASER phasing