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Crystal structure of uncleaved guinea pig L-asparaginase type III
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 6 293 0.1 M MES pH 6.0, 0.2 M ammonium sulfate, 13-15% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.83 67.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 114.872 α = 90 b = 114.872 β = 90 c = 138.971 γ = 120
Symmetry Space Group P 32 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 100 CCD MARMOSAIC 300 mm CCD 2013-04-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.97857 APS 21-ID-G
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 1.9 30 99.7 0.054 14.75 4.6 83861 83640
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 1.9 2.01 99.7 0.496 2.59 13338
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 (All) 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 1.9 28.73 78216 78216 4120 98.17 0.19413 0.19413 0.19309 0.21337 0.2488 RANDOM 43.04
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 0.02 0.02 -0.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.023 r_dihedral_angle_4_deg 15.069 r_dihedral_angle_3_deg 14.258 r_long_range_B_refined 7.291 r_long_range_B_other 7.284 r_dihedral_angle_1_deg 6.353 r_scangle_other 5.748 r_mcangle_other 4.251 r_mcangle_it 4.25 r_scbond_it 3.733
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.023 r_dihedral_angle_4_deg 15.069 r_dihedral_angle_3_deg 14.258 r_long_range_B_refined 7.291 r_long_range_B_other 7.284 r_dihedral_angle_1_deg 6.353 r_scangle_other 5.748 r_mcangle_other 4.251 r_mcangle_it 4.25 r_scbond_it 3.733 r_scbond_other 3.731 r_mcbond_it 3.119 r_mcbond_other 3.117 r_angle_refined_deg 1.575 r_angle_other_deg 0.825 r_chiral_restr 0.095 r_bond_refined_d 0.013 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4233 Nucleic Acid Atoms Solvent Atoms 178 Heterogen Atoms 2
Software Software Software Name Purpose CrystalClear data collection MOLREP phasing REFMAC refinement XDS data reduction XDS data scaling