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Crystal structure of the human L-asparaginase protein T219A 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 2.37 48.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.471 α = 90 b = 59.471 β = 90 c = 299.241 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 93 IMAGE PLATE RIGAKU RAXIS IV++ 2012-10-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.92 30 96.3 0.06 11.78 2.9 43516 43516
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.92 2.04 87.6 0.375 1.86
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 4GDV 1.92 29.59 40863 40863 2214 95.26 0.16719 0.16461 0.21481 0.2636 RANDOM 26.434
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] -3.2 -3.2 6.4
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.013 r_dihedral_angle_3_deg 19.315 r_dihedral_angle_4_deg 18.048 r_dihedral_angle_1_deg 7.805 r_long_range_B_refined 3.815 r_long_range_B_other 3.786 r_mcangle_it 2.375 r_mcangle_other 2.369 r_scangle_other 2.243 r_angle_refined_deg 1.741
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.013 r_dihedral_angle_3_deg 19.315 r_dihedral_angle_4_deg 18.048 r_dihedral_angle_1_deg 7.805 r_long_range_B_refined 3.815 r_long_range_B_other 3.786 r_mcangle_it 2.375 r_mcangle_other 2.369 r_scangle_other 2.243 r_angle_refined_deg 1.741 r_mcbond_it 1.695 r_mcbond_other 1.688 r_scbond_it 1.553 r_scbond_other 1.548 r_angle_other_deg 0.949 r_chiral_restr 0.099 r_bond_refined_d 0.012 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4270 Nucleic Acid Atoms Solvent Atoms 155 Heterogen Atoms 24
Software Software Software Name Purpose CrystalClear data collection MOLREP phasing REFMAC refinement XDS data reduction XDS data scaling