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Crystal Structure of Trigonal Form of D90E Mutant of Escherichia coli Asparaginase II
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3ECA Active dimer (AC) from native L-asparaginase II structure - PDB code: 3ECA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 292 sodium citrate, HEPES, PH 7.5, 292 K, VAPOR DIFFUSION, HANGING DROP
Crystal Properties Matthews coefficient Solvent content 2.7 54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 123.255 α = 90 b = 123.255 β = 90 c = 83.874 γ = 120
Symmetry Space Group P 31 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 290 IMAGE PLATE MARRESEARCH 1998-03-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE SIEMENS 1.54178
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.65 20 97.3 0.109 11.2 3 21080 21041 -3 54.3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.65 2.74 96.4 0.542 2.2 3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 Active dimer (AC) from native L-asparaginase II structure - PDB code: 3ECA 2.65 10 -3 19606 19606 1065 100 0.1686 0.1686 0.1664 0.2125 0.209 0.2446 RANDOM 19.42
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] -0.23 -0.12 -0.23 0.35
RMS Deviations Key Refinement Restraint Deviation p_planar_d 3.768 p_scangle_it 2.483 p_angle_d 1.535 p_scbond_it 1.486 p_mcangle_it 0.815 p_mcbond_it 0.437 p_chiral_restr 0.098 p_bond_d 0.014 p_plane_restr 0.005 p_angle_deg
RMS Deviations Key Refinement Restraint Deviation p_planar_d 3.768 p_scangle_it 2.483 p_angle_d 1.535 p_scbond_it 1.486 p_mcangle_it 0.815 p_mcbond_it 0.437 p_chiral_restr 0.098 p_bond_d 0.014 p_plane_restr 0.005 p_angle_deg p_hb_or_metal_coord p_singtor_nbd p_multtor_nbd p_xhyhbond_nbd p_xyhbond_nbd p_planar_tor p_staggered_tor p_orthonormal_tor p_transverse_tor p_special_tor
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4610 Nucleic Acid Atoms Solvent Atoms 54 Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling EPMR phasing REFMAC refinement