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The structure of HitB-HitD complex with a C4 pantetheine cross-linking probe
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6M01
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 Tris-HCl, sodium acetate, PEG 4000, PEG 400
Crystal Properties Matthews coefficient Solvent content 2.12 41.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.867 α = 90 b = 92.593 β = 100.69 c = 74.072 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 PILATUS3 6M 2021-10-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.00 Photon Factory BL-5A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.85 50 98.2 0.04 0.999 20.1 3 49388
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.85 1.89 0.392 0.743 2.4
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 1.85 46.34 46756 2631 98.21 0.1895 0.18767 0.22282 0.2171 RANDOM 30.469
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] -0.62 -0.35 0.9 -0.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.092 r_dihedral_angle_1_deg 6.01 r_dihedral_angle_2_deg 5.238 r_long_range_B_refined 5.004 r_long_range_B_other 4.94 r_scangle_other 2.982 r_mcangle_it 2.344 r_mcangle_other 2.344 r_scbond_it 1.791 r_scbond_other 1.791
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.092 r_dihedral_angle_1_deg 6.01 r_dihedral_angle_2_deg 5.238 r_long_range_B_refined 5.004 r_long_range_B_other 4.94 r_scangle_other 2.982 r_mcangle_it 2.344 r_mcangle_other 2.344 r_scbond_it 1.791 r_scbond_other 1.791 r_mcbond_it 1.386 r_mcbond_other 1.386 r_angle_other_deg 1.179 r_angle_refined_deg 1.116 r_chiral_restr 0.057 r_gen_planes_refined 0.004 r_bond_refined_d 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg 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 4409 Nucleic Acid Atoms Solvent Atoms 324 Heterogen Atoms 59
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling REFMAC phasing Coot model building