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Crystal structure of sulfate-bound human l-asparaginase protein
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4GDT pdb entry 4GDT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.27 293 0.2 M AMMONIUM IODIDE, 2.2 M AMMONIUM SULFATE, PH 5.27, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K
Crystal Properties Matthews coefficient Solvent content 2.25 45.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.22 α = 90 b = 59.22 β = 90 c = 298.5 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++ MIRRORS 2012-01-09 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 2.13 30 79.4 0.067 12.8 26285 26285
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 2.13 2.25 53.5 0.325 2.89 2.06
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 4GDT 2.13 30 24437 24437 1333 77.8 0.169 0.166 0.1686 0.222 0.2232 RANDOM 27.2
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] -0.18 -0.18 0.36
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.177 r_dihedral_angle_3_deg 17.438 r_dihedral_angle_4_deg 14.413 r_dihedral_angle_1_deg 6.19 r_scangle_it 2.033 r_scbond_it 1.584 r_angle_refined_deg 1.298 r_mcangle_it 0.874 r_mcbond_it 0.488 r_chiral_restr 0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.177 r_dihedral_angle_3_deg 17.438 r_dihedral_angle_4_deg 14.413 r_dihedral_angle_1_deg 6.19 r_scangle_it 2.033 r_scbond_it 1.584 r_angle_refined_deg 1.298 r_mcangle_it 0.874 r_mcbond_it 0.488 r_chiral_restr 0.08 r_bond_refined_d 0.01 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4257 Nucleic Acid Atoms Solvent Atoms 212 Heterogen Atoms 71
Software Software Software Name Purpose CrystalClear data collection MOLREP phasing REFMAC refinement XDS data reduction XDS data scaling