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Crystal structure of the human L-asparaginase protein T186V mutant
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 2.36 47.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.378 α = 90 b = 59.378 β = 90 c = 298.322 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 2012-10-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 1.0782 APS 21-ID-D
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 1.71 30 98.1 0.062 14.41 5.28 62537 62537
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 1.71 1.81 93.1 0.559 1.65 3.3
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 1.71 28.45 57400 57400 3066 94.88 0.17514 0.17247 0.1755 0.2252 0.2259 RANDOM 26.426
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] 0.41 0.41 -0.82
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.008 r_dihedral_angle_3_deg 17.986 r_dihedral_angle_4_deg 9.639 r_dihedral_angle_1_deg 6.97 r_long_range_B_refined 3.174 r_long_range_B_other 3.148 r_mcangle_it 2.092 r_mcangle_other 2.092 r_scangle_other 1.993 r_angle_refined_deg 1.603
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.008 r_dihedral_angle_3_deg 17.986 r_dihedral_angle_4_deg 9.639 r_dihedral_angle_1_deg 6.97 r_long_range_B_refined 3.174 r_long_range_B_other 3.148 r_mcangle_it 2.092 r_mcangle_other 2.092 r_scangle_other 1.993 r_angle_refined_deg 1.603 r_mcbond_it 1.498 r_mcbond_other 1.498 r_scbond_it 1.402 r_scbond_other 1.402 r_angle_other_deg 0.886 r_chiral_restr 0.087 r_bond_refined_d 0.011 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 4303 Nucleic Acid Atoms Solvent Atoms 177 Heterogen Atoms 2
Software Software Software Name Purpose CrystalClear data collection MOLREP phasing REFMAC refinement XDS data reduction XDS data scaling