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Structure of mBaoJin at pH 4.6
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 4.6 293 PEG3350, 0.2 M lithium sulfate, 0.1 M Na Acetate pH4.6
Crystal Properties Matthews coefficient Solvent content 2.06 40.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.447 α = 90 b = 78.919 β = 90 c = 84.434 γ = 90
Symmetry Space Group P 21 21 21
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 SEALED TUBE RIGAKU MICROMAX-003 1.54
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 1.8 25 99.6 0.99 6.98 3.2 41116
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 1.8 1.87 0.63
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 1.8 15 36375 1822 86.978 0.203 0.1986 0.2088 0.2845 0.2891 19.953
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] -0.207 2.152 -1.945
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.652 r_dihedral_angle_4_deg 19.105 r_dihedral_angle_3_deg 17.778 r_dihedral_angle_1_deg 9.264 r_lrange_it 6.623 r_lrange_other 6.402 r_scangle_it 4.455 r_scangle_other 4.455 r_mcangle_other 3.32 r_mcangle_it 3.319
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.652 r_dihedral_angle_4_deg 19.105 r_dihedral_angle_3_deg 17.778 r_dihedral_angle_1_deg 9.264 r_lrange_it 6.623 r_lrange_other 6.402 r_scangle_it 4.455 r_scangle_other 4.455 r_mcangle_other 3.32 r_mcangle_it 3.319 r_scbond_it 3.062 r_scbond_other 3.061 r_mcbond_it 2.401 r_mcbond_other 2.397 r_angle_refined_deg 2.273 r_angle_other_deg 1.463 r_nbd_other 0.387 r_symmetry_xyhbond_nbd_refined 0.354 r_xyhbond_nbd_refined 0.329 r_symmetry_nbd_refined 0.326 r_nbd_refined 0.229 r_symmetry_nbd_other 0.208 r_nbtor_refined 0.18 r_symmetry_xyhbond_nbd_other 0.166 r_chiral_restr 0.102 r_symmetry_nbtor_other 0.101 r_bond_refined_d 0.017 r_gen_planes_refined 0.015 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3443 Nucleic Acid Atoms Solvent Atoms 655 Heterogen Atoms 40
Software Software Software Name Purpose REFMAC refinement CrysalisPro data reduction CrysalisPro data scaling MOLREP phasing