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Structure of atypical asparaginase from Rhodospirillum rubrum in complex with L-Asp
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.2 uL 19 mg/mL protein in 50 mM HEPES, 150 mM sodium chloride + 0.2 uL reservoir (0.2 M magnesium chloride, 0.1 M HEPES, pH 7.5, 30% v/v PEG400, 20 mM L-Asp)
Crystal Properties Matthews coefficient Solvent content 1.9 35.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.46 α = 90 b = 76.126 β = 90 c = 55.362 γ = 90
Symmetry Space Group P 21 21 2
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 EIGER X 16M 2022-01-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.0 APS 22-ID
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 1.35 40 98.1 0.073 0.076 0.023 0.994 15.4 10.9 65882
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 1.35 1.37 85.3 0.846 0.948 0.413 0.647 4.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) 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 1.35 37.97 60006 1986 92.4 0.125 0.123 0.122 0.17 0.1696 RANDOM 17.37
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] -0.78 -0.75 1.53
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 22.77 r_dihedral_angle_4_deg 16.575 r_dihedral_angle_3_deg 12.899 r_dihedral_angle_1_deg 6.409 r_scangle_other 4.774 r_long_range_B_refined 4.221 r_rigid_bond_restr 4.137 r_scbond_other 4.076 r_scbond_it 4.073 r_long_range_B_other 3.999
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 22.77 r_dihedral_angle_4_deg 16.575 r_dihedral_angle_3_deg 12.899 r_dihedral_angle_1_deg 6.409 r_scangle_other 4.774 r_long_range_B_refined 4.221 r_rigid_bond_restr 4.137 r_scbond_other 4.076 r_scbond_it 4.073 r_long_range_B_other 3.999 r_mcangle_it 2.604 r_mcangle_other 2.604 r_mcbond_it 2.147 r_mcbond_other 2.146 r_angle_refined_deg 2.116 r_angle_other_deg 1.62 r_chiral_restr 0.126 r_bond_refined_d 0.017 r_gen_planes_refined 0.012 r_bond_other_d 0.001 r_gen_planes_other 0.001 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_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2437 Nucleic Acid Atoms Solvent Atoms 351 Heterogen Atoms 22
Software Software Software Name Purpose REFMAC refinement HKL-3000 data scaling HKL-2000 data reduction PHASER phasing