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Crystal structure of malonate-bound human L-asparaginase protein
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2ZAK pdb entry 2ZAK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 2.2M SODIUM MALONATE, PH 7.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K
Crystal Properties Matthews coefficient Solvent content 2.27 45.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.459 α = 90 b = 59.459 β = 90 c = 298.9 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 2011-11-11 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 1.85 30 94.7 0.047 18.4 48285 48285
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 1.85 1.96 69.5 0.249 2.58 1.9
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 2ZAK 1.85 29.73 45342 45342 2406 93.6 0.163 0.161 0.1625 0.204 0.1984 RANDOM 23.09
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] -3.91 -3.91 7.82
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.905 r_dihedral_angle_3_deg 15.418 r_dihedral_angle_4_deg 13.64 r_dihedral_angle_1_deg 5.956 r_scangle_it 1.906 r_scbond_it 1.255 r_angle_refined_deg 1.21 r_mcangle_it 0.858 r_mcbond_it 0.488 r_chiral_restr 0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.905 r_dihedral_angle_3_deg 15.418 r_dihedral_angle_4_deg 13.64 r_dihedral_angle_1_deg 5.956 r_scangle_it 1.906 r_scbond_it 1.255 r_angle_refined_deg 1.21 r_mcangle_it 0.858 r_mcbond_it 0.488 r_chiral_restr 0.08 r_bond_refined_d 0.009 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4309 Nucleic Acid Atoms Solvent Atoms 251 Heterogen Atoms 9
Software Software Software Name Purpose CrystalClear data collection MOLREP phasing REFMAC refinement XDS data reduction XDS data scaling