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Crystal structure of Rhizobium etli inducible L-asparaginase ReAV (monoclinic form MP1)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 292 25% PEG3350, 0.2 M Li2SO4, 0.1 M Tris pH 8.0, 20 mM n-octyl-beta-D-thioglucoside
Crystal Properties Matthews coefficient Solvent content 2.6 52.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.812 α = 90 b = 91.044 β = 97.075 c = 113.662 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 PIXEL DECTRIS PILATUS 6M 2019-04-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 0.9763 PETRA III, EMBL c/o DESY P13 (MX1)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 1.43 77.22 99.3 0.073 0.084 0.998 10.2 4.1 287575 22.93
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.43 1.52 96.8 0.818 0.952 0.671 1.5 3.4
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-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE XXXX 1.43 77.22 287572 1000 99.291 0.159 0.1585 0.1603 0.179 0.182 18.944
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] -0.678 0.703 -0.705 1.172
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.099 r_dihedral_angle_4_deg 14.708 r_dihedral_angle_3_deg 12.628 r_dihedral_angle_1_deg 6.283 r_lrange_it 4.817 r_lrange_other 4.734 r_scangle_it 2.977 r_scangle_other 2.977 r_scbond_it 1.927 r_scbond_other 1.927
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.099 r_dihedral_angle_4_deg 14.708 r_dihedral_angle_3_deg 12.628 r_dihedral_angle_1_deg 6.283 r_lrange_it 4.817 r_lrange_other 4.734 r_scangle_it 2.977 r_scangle_other 2.977 r_scbond_it 1.927 r_scbond_other 1.927 r_mcangle_it 1.846 r_mcangle_other 1.842 r_angle_refined_deg 1.681 r_angle_other_deg 1.521 r_mcbond_it 1.175 r_mcbond_other 1.169 r_nbd_other 0.217 r_nbd_refined 0.216 r_symmetry_xyhbond_nbd_refined 0.204 r_symmetry_nbd_refined 0.198 r_symmetry_nbd_other 0.18 r_xyhbond_nbd_refined 0.173 r_nbtor_refined 0.164 r_symmetry_xyhbond_nbd_other 0.122 r_chiral_restr 0.09 r_symmetry_nbtor_other 0.084 r_ncsr_local_group_3 0.073 r_ncsr_local_group_5 0.073 r_ncsr_local_group_2 0.072 r_ncsr_local_group_4 0.069 r_ncsr_local_group_6 0.059 r_ncsr_local_group_1 0.058 r_bond_refined_d 0.011 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10352 Nucleic Acid Atoms Solvent Atoms 1543 Heterogen Atoms 47
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing