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Crystal structure of the HC7 apo form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold We used the alphafold model generated by the AlphaFold2 server.
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 Lithium chloride
Tris
PEG 8000
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.854 α = 90 b = 93.854 β = 90 c = 87.287 γ = 90
Symmetry Space Group P 41 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 PILATUS3 S 6M 2022-01-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 0.9793 ALBA XALOC
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.75 93.85 91.9 0.034 11.5 8.7 36731
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 1.75 1.84 1.209 0.644
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 1.75 66.36 35169 1423 91.73 0.19293 0.19131 0.23117 0.2254 RANDOM 30.438
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] 0.19 0.19 -0.37
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.772 r_dihedral_angle_3_deg 14.483 r_dihedral_angle_4_deg 10.549 r_long_range_B_refined 7.546 r_long_range_B_other 7.541 r_dihedral_angle_1_deg 7.143 r_scangle_other 5.734 r_scbond_it 3.766 r_scbond_other 3.766 r_mcangle_other 3.46
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.772 r_dihedral_angle_3_deg 14.483 r_dihedral_angle_4_deg 10.549 r_long_range_B_refined 7.546 r_long_range_B_other 7.541 r_dihedral_angle_1_deg 7.143 r_scangle_other 5.734 r_scbond_it 3.766 r_scbond_other 3.766 r_mcangle_other 3.46 r_mcangle_it 3.457 r_mcbond_it 2.536 r_mcbond_other 2.523 r_angle_refined_deg 1.932 r_angle_other_deg 1.099 r_chiral_restr 0.164 r_bond_refined_d 0.019 r_gen_planes_refined 0.01 r_bond_other_d 0.002 r_gen_planes_other 0.002 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 2730 Nucleic Acid Atoms Solvent Atoms 168 Heterogen Atoms 6
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling PHASER phasing