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Structure of mBaoJin at pH 6.5
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8BXT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 288 PEG8000, 0.1M NH4Acetate, 0.1M Na Cocadilate pH 6.5
Crystal Properties Matthews coefficient Solvent content 2.59 52.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.5 α = 90 b = 120.31 β = 105.95 c = 52.8 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 DECTRIS PILATUS3 6M 2023-07-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NFPSS BEAMLINE BL19U1 0.97861 NFPSS BL19U1
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 1.45 30 97.7 0.99 15.8 6.3 94189
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 1.45 1.49 0.671
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.45 15 94058 4627 97.435 0.125 0.1228 0.1625 0.1369 21.4
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] 3.224 0.839 -2.048 -1.423
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.658 r_dihedral_angle_3_deg 13.115 r_dihedral_angle_1_deg 7.724 r_dihedral_angle_4_deg 6.968 r_lrange_it 5.719 r_lrange_other 5.293 r_scangle_it 4.428 r_scangle_other 4.427 r_rigid_bond_restr 3.856 r_scbond_it 3.818
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.658 r_dihedral_angle_3_deg 13.115 r_dihedral_angle_1_deg 7.724 r_dihedral_angle_4_deg 6.968 r_lrange_it 5.719 r_lrange_other 5.293 r_scangle_it 4.428 r_scangle_other 4.427 r_rigid_bond_restr 3.856 r_scbond_it 3.818 r_scbond_other 3.817 r_mcangle_other 3.489 r_mcangle_it 3.485 r_mcbond_it 2.708 r_mcbond_other 2.683 r_angle_refined_deg 1.901 r_angle_other_deg 1.481 r_nbd_other 0.308 r_symmetry_nbd_refined 0.225 r_symmetry_nbd_other 0.206 r_nbd_refined 0.199 r_symmetry_xyhbond_nbd_refined 0.194 r_nbtor_refined 0.174 r_symmetry_xyhbond_nbd_other 0.161 r_xyhbond_nbd_refined 0.144 r_symmetry_nbtor_other 0.093 r_chiral_restr 0.087 r_bond_refined_d 0.013 r_gen_planes_refined 0.012 r_bond_other_d 0.005 r_gen_planes_other 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3438 Nucleic Acid Atoms Solvent Atoms 681 Heterogen Atoms 40
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing