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Structure of mBaoJin at pH 8.5
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8Q79
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 PEG 3350, 0.2M Lithium Sulfate, 0.1M Tris-Cl pH 8.5
Crystal Properties Matthews coefficient Solvent content 2.6 52.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.59 α = 90 b = 120.266 β = 105.489 c = 52.903 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 PIXEL RIGAKU HyPix-6000HE 2023-07-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.6 23.47 96.2 0.99 14.5 2.8 72205
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.6 1.66 95.4 0.69
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.6 15 69357 3524 96.106 0.188 0.1855 0.1971 0.2292 0.2396 14.497
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] 1.266 0.09 -0.51 -0.7
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.029 r_dihedral_angle_3_deg 15.663 r_dihedral_angle_4_deg 14.051 r_dihedral_angle_1_deg 7.959 r_lrange_it 6.833 r_lrange_other 6.433 r_scangle_it 3.954 r_scangle_other 3.935 r_mcangle_other 3.023 r_mcangle_it 3.021
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.029 r_dihedral_angle_3_deg 15.663 r_dihedral_angle_4_deg 14.051 r_dihedral_angle_1_deg 7.959 r_lrange_it 6.833 r_lrange_other 6.433 r_scangle_it 3.954 r_scangle_other 3.935 r_mcangle_other 3.023 r_mcangle_it 3.021 r_scbond_it 2.497 r_scbond_other 2.484 r_angle_refined_deg 1.991 r_mcbond_it 1.851 r_mcbond_other 1.833 r_angle_other_deg 1.472 r_symmetry_xyhbond_nbd_refined 0.283 r_nbd_other 0.226 r_xyhbond_nbd_refined 0.213 r_nbd_refined 0.205 r_symmetry_nbd_other 0.197 r_symmetry_nbd_refined 0.188 r_nbtor_refined 0.176 r_symmetry_xyhbond_nbd_other 0.122 r_symmetry_nbtor_other 0.095 r_chiral_restr 0.088 r_bond_refined_d 0.014 r_gen_planes_refined 0.013 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3430 Nucleic Acid Atoms Solvent Atoms 791 Heterogen Atoms 50
Software Software Software Name Purpose REFMAC refinement CrysalisPro data reduction Aimless data scaling MOLREP phasing