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Crystal structure of Rhizobium etli inducible L-asparaginase ReAV (orthorhombic form OP)
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 2.39 48.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.231 α = 90 b = 91.142 β = 90 c = 106.017 γ = 90
Symmetry Space Group P 21 21 21
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) 0.9762 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) Rpim 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 1.29 69.11 95.4 0.17 0.179 0.05 0.996 10.4 12.7 131038 19.77
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.29 1.4 64.7 2.008 2.113 0.639 0.4 1.5 10.4
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 7OS3 1.293 69.11 129695 1000 68.626 0.155 0.1547 0.1546 0.1943 0.1931 RANDOM 13.957
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] 0.99 0.012 -1.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.227 r_dihedral_angle_4_deg 18.097 r_dihedral_angle_3_deg 12.404 r_rigid_bond_restr 6.399 r_dihedral_angle_1_deg 6.237 r_lrange_it 4.522 r_lrange_other 4.345 r_scangle_it 3.869 r_scangle_other 3.748 r_scbond_it 3.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.227 r_dihedral_angle_4_deg 18.097 r_dihedral_angle_3_deg 12.404 r_rigid_bond_restr 6.399 r_dihedral_angle_1_deg 6.237 r_lrange_it 4.522 r_lrange_other 4.345 r_scangle_it 3.869 r_scangle_other 3.748 r_scbond_it 3.26 r_scbond_other 3.16 r_mcangle_it 2.325 r_mcangle_other 2.324 r_mcbond_it 1.822 r_mcbond_other 1.814 r_angle_refined_deg 1.626 r_angle_other_deg 1.554 r_nbd_refined 0.213 r_nbd_other 0.202 r_symmetry_nbd_other 0.179 r_xyhbond_nbd_refined 0.177 r_symmetry_nbd_refined 0.167 r_nbtor_refined 0.164 r_metal_ion_refined 0.129 r_symmetry_xyhbond_nbd_refined 0.117 r_chiral_restr 0.09 r_symmetry_nbtor_other 0.082 r_ncsr_local_group_1 0.081 r_bond_refined_d 0.012 r_gen_planes_refined 0.01 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5303 Nucleic Acid Atoms Solvent Atoms 628 Heterogen Atoms 61
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing