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Crystal structure of Rhizobium etli inducible L-asparaginase ReAV (monoclinic form MP2)
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 6.5 292 2% PEG8000, 20% PEG400, 5 mM Mg(CH3COO)2, 6 mM 3.0 mM sucrose monolaureate
Crystal Properties Matthews coefficient Solvent content 2.55 51.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.923 α = 90 b = 91.308 β = 97.111 c = 114.164 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 225 mm CCD 2019-12-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.3 0.8950 BESSY 14.3
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.65 45.65 99 0.134 0.995 10 4 189888 21.54
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 1.65 1.75 98 0.622 0.795 2.2 4.1
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 7OS3 1.65 45.65 189888 1000 99.048 0.19 0.1898 0.2023 0.2217 0.2357 16.259
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] -0.931 0.344 -0.671 1.47
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.435 r_dihedral_angle_4_deg 14.74 r_dihedral_angle_3_deg 13.289 r_dihedral_angle_1_deg 6.404 r_lrange_it 4.596 r_lrange_other 4.545 r_scangle_it 2.636 r_scangle_other 2.636 r_scbond_it 1.702 r_scbond_other 1.702
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.435 r_dihedral_angle_4_deg 14.74 r_dihedral_angle_3_deg 13.289 r_dihedral_angle_1_deg 6.404 r_lrange_it 4.596 r_lrange_other 4.545 r_scangle_it 2.636 r_scangle_other 2.636 r_scbond_it 1.702 r_scbond_other 1.702 r_mcangle_it 1.697 r_mcangle_other 1.687 r_angle_refined_deg 1.645 r_angle_other_deg 1.509 r_mcbond_it 1.079 r_mcbond_other 1.068 r_nbd_refined 0.212 r_nbd_other 0.211 r_symmetry_xyhbond_nbd_refined 0.198 r_symmetry_nbd_other 0.184 r_nbtor_refined 0.16 r_symmetry_nbd_refined 0.157 r_xyhbond_nbd_refined 0.156 r_symmetry_xyhbond_nbd_other 0.108 r_chiral_restr 0.091 r_symmetry_nbtor_other 0.082 r_ncsr_local_group_5 0.082 r_ncsr_local_group_6 0.079 r_ncsr_local_group_1 0.077 r_ncsr_local_group_4 0.077 r_ncsr_local_group_2 0.074 r_ncsr_local_group_3 0.058 r_bond_refined_d 0.013 r_gen_planes_refined 0.01 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10372 Nucleic Acid Atoms Solvent Atoms 1403 Heterogen Atoms 8
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing