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Crystal structure of Rhizobium etli inducible L-asparaginase ReAV (monoclinic form MC)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7OS3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 292 25% PEG3350, 0.2 M Li2SO4, 0.01% (w/v) heptane-1,2,3-triol, 0.1 M Tris pH 8.0
Crystal Properties Matthews coefficient Solvent content 2.61 52.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 130.289 α = 90 b = 87.283 β = 130.154 c = 93.925 γ = 90
Symmetry Space Group C 1 2 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 PIXEL DECTRIS PILATUS 6M 2019-04-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.9184 BESSY 14.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) CC (Half) 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 1.757 46.732 98.3 0.042 1 22.04 6.74 78980 36.405
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.76 1.86 95.7 0.556 0.925 2.69 6.59
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 (All) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 7OS3 1.757 46.732 78974 1000 98.682 0.184 0.1832 0.2271 0.2233 32.962
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] -1.872 -0.701 -0.931 1.645
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.004 r_dihedral_angle_4_deg 19.189 r_dihedral_angle_3_deg 14.868 r_dihedral_angle_1_deg 7.096 r_lrange_it 5.535 r_lrange_other 5.535 r_scangle_it 4.196 r_scangle_other 4.195 r_mcangle_it 2.797 r_mcangle_other 2.797
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.004 r_dihedral_angle_4_deg 19.189 r_dihedral_angle_3_deg 14.868 r_dihedral_angle_1_deg 7.096 r_lrange_it 5.535 r_lrange_other 5.535 r_scangle_it 4.196 r_scangle_other 4.195 r_mcangle_it 2.797 r_mcangle_other 2.797 r_scbond_it 2.77 r_scbond_other 2.77 r_mcbond_it 2.041 r_mcbond_other 2.036 r_angle_refined_deg 1.652 r_angle_other_deg 1.483 r_nbd_refined 0.22 r_nbd_other 0.208 r_symmetry_nbd_refined 0.201 r_symmetry_nbd_other 0.192 r_xyhbond_nbd_refined 0.187 r_nbtor_refined 0.17 r_symmetry_xyhbond_nbd_refined 0.085 r_symmetry_nbtor_other 0.083 r_chiral_restr 0.074 r_bond_refined_d 0.015 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5359 Nucleic Acid Atoms Solvent Atoms 333 Heterogen Atoms 16
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing