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Crystal structure of partially-cleaved human l-asparaginase protein in complex with l-aspartate
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 7 293 2.2M SODIUM MALONATE, PH 7.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K
Crystal Properties Matthews coefficient Solvent content 2.28 45.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.5 α = 90 b = 59.5 β = 90 c = 299.5 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 2012-01-17 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 1.75 30 99.2 0.061 17.3 59545 59545
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 1.75 1.8 96.1 0.314 2.02 1.04
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 4GDT 1.75 30 56548 2996 99.1 0.161 0.159 0.191 0.1928 RANDOM 13.05
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] -0.63 -0.63 1.25
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.064 r_dihedral_angle_4_deg 15.394 r_dihedral_angle_3_deg 14.712 r_dihedral_angle_1_deg 6.109 r_scangle_it 2.616 r_scbond_it 1.666 r_angle_refined_deg 1.268 r_mcangle_it 1.094 r_mcbond_it 0.628 r_chiral_restr 0.082
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.064 r_dihedral_angle_4_deg 15.394 r_dihedral_angle_3_deg 14.712 r_dihedral_angle_1_deg 6.109 r_scangle_it 2.616 r_scbond_it 1.666 r_angle_refined_deg 1.268 r_mcangle_it 1.094 r_mcbond_it 0.628 r_chiral_restr 0.082 r_bond_refined_d 0.01 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4314 Nucleic Acid Atoms Solvent Atoms 263 Heterogen Atoms 20
Software Software Software Name Purpose CrystalClear data collection MOLREP phasing REFMAC refinement XDS data reduction XDS data scaling