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Structure of atypical asparaginase from Rhodospirillum rubrum
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
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 + 0.2 uL reservoir (0.2 M magnesium chloride, 0.1 M HEPES, pH 7.5, 30% v/v PEG400)
Crystal Properties Matthews coefficient Solvent content 2.03 39.43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.184 α = 90 b = 76.962 β = 90 c = 57.815 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 1.65 40 95.2 0.098 0.104 0.033 0.996 7.9 10 37670
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 1.66 1.69 92.9 0.986 1.051 0.347 0.719 6.6
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.65 38.96 32023 1710 84.88 0.18789 0.18606 0.22241 0.2384 RANDOM 17.365
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] 0.07 -0.24 0.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 21.064 r_dihedral_angle_4_deg 15.851 r_dihedral_angle_3_deg 13.424 r_dihedral_angle_1_deg 6.718 r_long_range_B_refined 5.386 r_long_range_B_other 5.316 r_scangle_other 4.022 r_scbond_it 2.558 r_scbond_other 2.557 r_mcangle_it 2.529
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 21.064 r_dihedral_angle_4_deg 15.851 r_dihedral_angle_3_deg 13.424 r_dihedral_angle_1_deg 6.718 r_long_range_B_refined 5.386 r_long_range_B_other 5.316 r_scangle_other 4.022 r_scbond_it 2.558 r_scbond_other 2.557 r_mcangle_it 2.529 r_mcangle_other 2.529 r_angle_refined_deg 1.652 r_mcbond_it 1.647 r_mcbond_other 1.641 r_angle_other_deg 1.47 r_chiral_restr 0.081 r_bond_refined_d 0.011 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 2413 Nucleic Acid Atoms Solvent Atoms 229 Heterogen Atoms 14
Software Software Software Name Purpose REFMAC refinement HKL-3000 data scaling HKL-2000 data reduction PHASER phasing