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High resolution crystal structure of uncleaved human L-asparaginase protein
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 2.34 47.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.213 α = 90 b = 59.213 β = 90 c = 297.793 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 100 CCD MARMOSAIC 300 mm CCD 2013-08-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.97856 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 1.5 30 99 0.092 13.2 8.1 92426 92426
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 1.5 1.59 94.3 0.348 2.86 4.1 14240
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 1.5 29.04 84429 84429 4425 95.19 0.15465 0.152 0.159 0.20529 0.2106 RANDOM 15.844
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] -8.46 -8.46 16.91
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.621 r_dihedral_angle_3_deg 14.282 r_dihedral_angle_4_deg 12.289 r_sphericity_free 9.051 r_dihedral_angle_1_deg 6.562 r_sphericity_bonded 4.73 r_rigid_bond_restr 2.499 r_long_range_B_refined 2.16 r_long_range_B_other 2.122 r_scangle_other 2.004
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.621 r_dihedral_angle_3_deg 14.282 r_dihedral_angle_4_deg 12.289 r_sphericity_free 9.051 r_dihedral_angle_1_deg 6.562 r_sphericity_bonded 4.73 r_rigid_bond_restr 2.499 r_long_range_B_refined 2.16 r_long_range_B_other 2.122 r_scangle_other 2.004 r_mcangle_it 1.894 r_mcangle_other 1.894 r_scbond_it 1.842 r_scbond_other 1.841 r_mcbond_it 1.751 r_mcbond_other 1.751 r_angle_refined_deg 1.559 r_angle_other_deg 0.832 r_chiral_restr 0.088 r_bond_refined_d 0.012 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4222 Nucleic Acid Atoms Solvent Atoms 339 Heterogen Atoms 15
Software Software Software Name Purpose CrystalClear data collection MOLREP phasing REFMAC refinement XDS data reduction XDS data scaling