6RGY | pdb_00006rgy

Revisiting pH-gated conformational switch. Complex HK853-RR468 pH 7.5


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.52941,8M HH4SO4, 0,1M citrato 7,5
Crystal Properties
Matthews coefficientSolvent content
3.261.54

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 68.47α = 90
b = 92.71β = 93.39
c = 174.522γ = 90
Symmetry
Space GroupI 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2018-02-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.97927DiamondI04

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
12.287.1199.80.0550.99911.63.855215
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.22.260.539

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB 3DGE2.287.1152418279399.740.187670.185510.20.226940.23RANDOM57.273
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]
-2.280.442.31-0.08
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.807
r_dihedral_angle_4_deg20.763
r_dihedral_angle_3_deg16.881
r_long_range_B_other6.553
r_long_range_B_refined6.552
r_scangle_other4.67
r_scbond_it3.092
r_scbond_other3.086
r_mcangle_it3.059
r_mcangle_other3.059
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.807
r_dihedral_angle_4_deg20.763
r_dihedral_angle_3_deg16.881
r_long_range_B_other6.553
r_long_range_B_refined6.552
r_scangle_other4.67
r_scbond_it3.092
r_scbond_other3.086
r_mcangle_it3.059
r_mcangle_other3.059
r_mcbond_it2.046
r_mcbond_other2.046
r_angle_refined_deg2.033
r_angle_other_deg1.111
r_chiral_restr0.12
r_bond_refined_d0.019
r_gen_planes_refined0.008
r_bond_other_d0.003
r_gen_planes_other0.002
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 AtomsNumber
Protein Atoms5536
Nucleic Acid Atoms
Solvent Atoms309
Heterogen Atoms134

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing