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Revisiting pH-gated conformational switch. Complex HK853-RR468 pH 5.5
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 5.5 294 1,5 M HH4SO4, 0,1M bis-tris 5,5
Crystal Properties Matthews coefficient Solvent content 3.21 61.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.616 α = 90 b = 92.933 β = 93.49 c = 174.337 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 PILATUS 6M 2019-02-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 0.979178 ALBA XALOC
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 2.87 49.21 97.6 0.998 14.1 3.8 24443
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.87 3.03
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 2.87 49.21 23163 1279 97.24 0.24271 0.24024 0.2406 0.28727 0.2849 RANDOM 63.475
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] -3.22 0.96 4.19 -1.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.877 r_dihedral_angle_3_deg 15.084 r_dihedral_angle_4_deg 12.912 r_dihedral_angle_1_deg 4.667 r_long_range_B_refined 2.53 r_long_range_B_other 2.381 r_angle_refined_deg 1.022 r_angle_other_deg 0.844 r_mcangle_it 0.473 r_mcangle_other 0.473
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.877 r_dihedral_angle_3_deg 15.084 r_dihedral_angle_4_deg 12.912 r_dihedral_angle_1_deg 4.667 r_long_range_B_refined 2.53 r_long_range_B_other 2.381 r_angle_refined_deg 1.022 r_angle_other_deg 0.844 r_mcangle_it 0.473 r_mcangle_other 0.473 r_scangle_other 0.285 r_mcbond_it 0.252 r_mcbond_other 0.252 r_scbond_it 0.149 r_scbond_other 0.143 r_chiral_restr 0.054 r_bond_refined_d 0.007 r_gen_planes_refined 0.002 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 5543 Nucleic Acid Atoms Solvent Atoms 173 Heterogen Atoms 116
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing