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Crystal structure of the guinea pig L-asparaginase 1 catalytic domain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2HIM PDB entry 2HIM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 293 0.1 M HEPES, 15% PEG 4000, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.18 43.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 98.55 α = 90 b = 123.31 β = 92.35 c = 120.56 γ = 90
Symmetry Space Group P 1 21 1
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 2013-06-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G APS 21-ID-G
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.2 120.46 99.7 146207
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.34 98.5
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 2HIM 2.2 29.617 145526 138245 7281 99.18 0.20849 0.20694 0.2121 0.238 0.2429 RANDOM 37.191
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] 0.44 -0.18 0.41 -0.83
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.902 r_dihedral_angle_4_deg 19.817 r_dihedral_angle_3_deg 12.983 r_long_range_B_refined 7.94 r_long_range_B_other 7.936 r_scangle_other 5.836 r_dihedral_angle_1_deg 5.823 r_mcangle_other 4.892 r_mcangle_it 4.571 r_scbond_other 3.574
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.902 r_dihedral_angle_4_deg 19.817 r_dihedral_angle_3_deg 12.983 r_long_range_B_refined 7.94 r_long_range_B_other 7.936 r_scangle_other 5.836 r_dihedral_angle_1_deg 5.823 r_mcangle_other 4.892 r_mcangle_it 4.571 r_scbond_other 3.574 r_scbond_it 3.029 r_mcbond_it 2.779 r_mcbond_other 2.778 r_angle_refined_deg 1.339 r_angle_other_deg 1.065 r_chiral_restr 0.072 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 r_bond_other_d 0.006 r_gen_planes_other 0.005 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 21650 Nucleic Acid Atoms Solvent Atoms 892 Heterogen Atoms 120
Software Software Software Name Purpose CrystalClear data collection MOLREP phasing REFMAC refinement XDS data reduction XDS data scaling