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Structure of atypical asparaginase from Rhodospirillum rubrum (mutant Y21F)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.2 uL 18 mg/mL protein in 50 mM HEPES, pH 7, 150 mM sodium chloride + 0.2 uL reservoir (Molecular Dimensions Morpheus A2, pH 6.5)
Crystal Properties Matthews coefficient Solvent content 2.22 44.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 245.644 α = 90 b = 63.185 β = 103.42 c = 92.968 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 EIGER X 16M 2021-10-05 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 1.75 40 97.1 0.08 0.092 0.043 0.994 11.6 4.1 132560
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 1.75 1.78 97 0.994 1.145 0.56 0.627 3.9
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 1.76 39.4 127611 1657 94.26 0.16498 0.16434 0.1753 0.21599 0.2234 RANDOM 22.123
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] -0.04 0.02 0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 19.331 r_dihedral_angle_4_deg 16.614 r_dihedral_angle_3_deg 12.581 r_dihedral_angle_1_deg 6.808 r_long_range_B_refined 6.759 r_long_range_B_other 6.648 r_scangle_other 4.983 r_scbond_it 3.216 r_scbond_other 3.216 r_mcangle_it 3.116
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 19.331 r_dihedral_angle_4_deg 16.614 r_dihedral_angle_3_deg 12.581 r_dihedral_angle_1_deg 6.808 r_long_range_B_refined 6.759 r_long_range_B_other 6.648 r_scangle_other 4.983 r_scbond_it 3.216 r_scbond_other 3.216 r_mcangle_it 3.116 r_mcangle_other 3.116 r_mcbond_it 2.162 r_mcbond_other 2.162 r_angle_refined_deg 1.741 r_angle_other_deg 1.469 r_chiral_restr 0.087 r_bond_refined_d 0.012 r_gen_planes_refined 0.009 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9631 Nucleic Acid Atoms Solvent Atoms 1076 Heterogen Atoms 129
Software Software Software Name Purpose REFMAC refinement HKL-3000 data scaling HKL-2000 data reduction PHASER phasing