6RF3

Crystal structure of the potassium-pumping G263F mutant of the light-driven sodium pump KR2 in the pentameric form, pH 8.0


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6REW 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1LIPIDIC CUBIC PHASE2933.4 M Sodium Malonate pH 8.0
Crystal Properties
Matthews coefficientSolvent content
3.4163.9

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 131.68α = 90
b = 239.685β = 90
c = 134.584γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2018-02-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID291.003ESRFID29

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)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
12.447.971000.1310.1420.0550.99810.36.783371
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.42.451002.2832.4670.9280.4257

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 REPLACEMENTTHROUGHOUT6REW2.447.9778915419599.910.17410.17250.2046RANDOM54.155
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]
3.71-5.511.8
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.772
r_dihedral_angle_4_deg22.149
r_dihedral_angle_3_deg16.218
r_dihedral_angle_1_deg7.398
r_angle_other_deg0.751
r_angle_refined_deg0.704
r_chiral_restr0.04
r_bond_refined_d0.003
r_gen_planes_refined0.003
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.772
r_dihedral_angle_4_deg22.149
r_dihedral_angle_3_deg16.218
r_dihedral_angle_1_deg7.398
r_angle_other_deg0.751
r_angle_refined_deg0.704
r_chiral_restr0.04
r_bond_refined_d0.003
r_gen_planes_refined0.003
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms10977
Nucleic Acid Atoms
Solvent Atoms462
Heterogen Atoms1653

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
MOLREPphasing