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Crystal structure of human L-asparaginase protein with covalently linked substrate L-asparagine
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 2.38 48.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.651 α = 90 b = 59.651 β = 90 c = 298.517 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++ 2012-05-25 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 1.97 30 91.9 0.097 9.16 3.36 38615 38615
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 1.97 2.09 80.5 0.435 2.05 3.07
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 1.97 29.83 35707 35716 1794 89.37 0.16881 0.16565 0.1656 0.23139 0.2302 RANDOM 26.228
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] -7.9 -7.9 15.81
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.503 r_dihedral_angle_3_deg 18.5 r_dihedral_angle_4_deg 17.275 r_dihedral_angle_1_deg 7.951 r_long_range_B_refined 3.34 r_long_range_B_other 3.291 r_mcangle_other 2.076 r_mcangle_it 2.048 r_scangle_other 2.005 r_angle_refined_deg 1.655
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.503 r_dihedral_angle_3_deg 18.5 r_dihedral_angle_4_deg 17.275 r_dihedral_angle_1_deg 7.951 r_long_range_B_refined 3.34 r_long_range_B_other 3.291 r_mcangle_other 2.076 r_mcangle_it 2.048 r_scangle_other 2.005 r_angle_refined_deg 1.655 r_scbond_it 1.524 r_mcbond_other 1.478 r_scbond_other 1.459 r_mcbond_it 1.376 r_chiral_restr 0.103 r_bond_refined_d 0.011 r_gen_planes_refined 0.007 r_gen_planes_other 0.003 r_bond_other_d r_angle_other_deg r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4294 Nucleic Acid Atoms Solvent Atoms 193 Heterogen Atoms 18
Software Software Software Name Purpose CrystalClear data collection MOLREP phasing REFMAC refinement XDS data reduction XDS data scaling