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Revisiting pH-gated conformational switch. Complex HK853-RR468 D53A 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 NH4SO4, citrato pH 7
Crystal Properties Matthews coefficient Solvent content 3.17 61.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.367 α = 90 b = 91.146 β = 93.6 c = 176.145 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 2018-04-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 0.979260 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 87.9 98 0.998 10.4 5.7 71301
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 2.04
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 87.9 67733 3563 97.78 0.21377 0.21154 0.2254 0.2551 0.265 RANDOM 49.632
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] -2.99 0.35 3.02 -0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.036 r_dihedral_angle_3_deg 15.939 r_dihedral_angle_4_deg 14.181 r_long_range_B_refined 8.794 r_long_range_B_other 8.766 r_scangle_other 6.707 r_dihedral_angle_1_deg 6.097 r_mcangle_it 4.796 r_mcangle_other 4.795 r_scbond_it 4.314
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.036 r_dihedral_angle_3_deg 15.939 r_dihedral_angle_4_deg 14.181 r_long_range_B_refined 8.794 r_long_range_B_other 8.766 r_scangle_other 6.707 r_dihedral_angle_1_deg 6.097 r_mcangle_it 4.796 r_mcangle_other 4.795 r_scbond_it 4.314 r_scbond_other 4.248 r_mcbond_it 3.345 r_mcbond_other 3.344 r_angle_refined_deg 1.581 r_angle_other_deg 0.966 r_chiral_restr 0.084 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 r_bond_other_d 0.002 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 5524 Nucleic Acid Atoms Solvent Atoms 348 Heterogen Atoms 104
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing