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Revisiting pH-gated conformational switch. Complex HK853-RR468 D53A pH 5.3
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 5.3 294 1,2 M NH4SO4, 0,1M Bistris pH 5,3
Crystal Properties Matthews coefficient Solvent content 3.21 61.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.532 α = 90 b = 92.134 β = 93.48 c = 175.932 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 87.8 99.5 0.998 13.5 3.7 73361
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 87.8 69680 3676 99.41 0.19416 0.19235 0.2043 0.22753 0.2353 RANDOM 41.518
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] -1.25 -0.06 1.79 -0.53
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.919 r_sphericity_free 26.341 r_dihedral_angle_4_deg 13.93 r_dihedral_angle_3_deg 13.094 r_sphericity_bonded 6.531 r_dihedral_angle_1_deg 5.152 r_long_range_B_refined 3.273 r_long_range_B_other 2.916 r_mcangle_it 2.46 r_mcangle_other 2.46
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.919 r_sphericity_free 26.341 r_dihedral_angle_4_deg 13.93 r_dihedral_angle_3_deg 13.094 r_sphericity_bonded 6.531 r_dihedral_angle_1_deg 5.152 r_long_range_B_refined 3.273 r_long_range_B_other 2.916 r_mcangle_it 2.46 r_mcangle_other 2.46 r_mcbond_it 1.843 r_mcbond_other 1.843 r_scangle_other 1.813 r_scbond_it 1.515 r_scbond_other 1.489 r_angle_refined_deg 1.127 r_angle_other_deg 0.852 r_rigid_bond_restr 0.847 r_chiral_restr 0.059 r_bond_refined_d 0.007 r_gen_planes_refined 0.003 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5521 Nucleic Acid Atoms Solvent Atoms 352 Heterogen Atoms 114
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing