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Crystal structure of the human L-asparaginase protein T168S mutant
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4GDV PDB entry 4GDV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 2.2-2.5 M sodium Malonate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.39 48.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.7 α = 90 b = 59.7 β = 90 c = 299.7 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MARMOSAIC 300 mm CCD 2012-03-07 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) 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 1.95 30 82.6 0.106 11.75 5.89 36456 36456
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 1.95 2 71.4 0.523 3.18 2.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 PDB entry 4GDV 1.95 29.27 33541 33541 1772 80.84 0.17803 0.17502 0.179 0.23401 0.235 RANDOM 19.645
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] -3.49 -3.49 6.98
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.571 r_dihedral_angle_3_deg 17.354 r_dihedral_angle_4_deg 13.499 r_dihedral_angle_1_deg 6.902 r_long_range_B_refined 3.4 r_long_range_B_other 3.4 r_mcangle_it 1.723 r_mcangle_other 1.722 r_scangle_other 1.676 r_angle_refined_deg 1.591
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.571 r_dihedral_angle_3_deg 17.354 r_dihedral_angle_4_deg 13.499 r_dihedral_angle_1_deg 6.902 r_long_range_B_refined 3.4 r_long_range_B_other 3.4 r_mcangle_it 1.723 r_mcangle_other 1.722 r_scangle_other 1.676 r_angle_refined_deg 1.591 r_mcbond_it 1.106 r_mcbond_other 1.102 r_scbond_it 1.088 r_scbond_other 1.088 r_angle_other_deg 0.871 r_chiral_restr 0.09 r_bond_refined_d 0.012 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4330 Nucleic Acid Atoms Solvent Atoms 216 Heterogen Atoms 22
Software Software Software Name Purpose CrystalClear data collection MOLREP phasing REFMAC refinement XDS data reduction XSCALE data scaling