6RH0

Revisiting pH-gated conformational switch. Complex HK853-RR468 pH 5.5


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3DGEPDB 3DGE

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.52941,5 M HH4SO4, 0,1M bis-tris 5,5
Crystal Properties
Matthews coefficientSolvent content
3.2161.67

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 68.616α = 90
b = 92.933β = 93.49
c = 174.337γ = 90
Symmetry
Space GroupI 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2019-02-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALBA BEAMLINE XALOC0.979178ALBAXALOC

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)CC (Half)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.8749.2197.60.99814.13.824443
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.873.03

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB 3DGE2.8749.2123163127997.240.242710.240240.28727RANDOM63.475
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]
-3.220.964.19-1.07
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.877
r_dihedral_angle_3_deg15.084
r_dihedral_angle_4_deg12.912
r_dihedral_angle_1_deg4.667
r_long_range_B_refined2.53
r_long_range_B_other2.381
r_angle_refined_deg1.022
r_angle_other_deg0.844
r_mcangle_it0.473
r_mcangle_other0.473
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.877
r_dihedral_angle_3_deg15.084
r_dihedral_angle_4_deg12.912
r_dihedral_angle_1_deg4.667
r_long_range_B_refined2.53
r_long_range_B_other2.381
r_angle_refined_deg1.022
r_angle_other_deg0.844
r_mcangle_it0.473
r_mcangle_other0.473
r_scangle_other0.285
r_mcbond_it0.252
r_mcbond_other0.252
r_scbond_it0.149
r_scbond_other0.143
r_chiral_restr0.054
r_bond_refined_d0.007
r_gen_planes_refined0.002
r_bond_other_d0.001
r_gen_planes_other0.001
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 AtomsNumber
Protein Atoms5543
Nucleic Acid Atoms
Solvent Atoms173
Heterogen Atoms116

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing