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Revisiting pH-gated conformational switch. Complex HK853-RR468 pH 7
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3DGE PDB 3DGE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 294 1,8 M HH4SO4, 0,1 M citrato pH 7
Crystal Properties Matthews coefficient Solvent content 3.2 61.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.673 α = 90 b = 93.579 β = 93.32 c = 172.703 γ = 90
Symmetry Space Group I 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 EIGER X 16M 2018-02-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.979270 Diamond I04
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 2.83 28.76 95 0.119 6 2.9 24854
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.83 2.98 0.451
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB 3DGE 2.83 30 23662 1189 95.04 0.24606 0.24284 0.2468 0.30923 0.3114 RANDOM 65.463
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] -2.17 0.4 2 0.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.089 r_dihedral_angle_3_deg 19.166 r_dihedral_angle_4_deg 18.458 r_dihedral_angle_1_deg 7.047 r_long_range_B_refined 4.97 r_long_range_B_other 4.521 r_mcangle_it 1.667 r_mcangle_other 1.667 r_angle_refined_deg 1.571 r_scangle_other 1.496
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.089 r_dihedral_angle_3_deg 19.166 r_dihedral_angle_4_deg 18.458 r_dihedral_angle_1_deg 7.047 r_long_range_B_refined 4.97 r_long_range_B_other 4.521 r_mcangle_it 1.667 r_mcangle_other 1.667 r_angle_refined_deg 1.571 r_scangle_other 1.496 r_scbond_it 1.003 r_angle_other_deg 0.992 r_mcbond_it 0.956 r_mcbond_other 0.956 r_scbond_other 0.874 r_chiral_restr 0.08 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 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 5481 Nucleic Acid Atoms Solvent Atoms 172 Heterogen Atoms 134
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing