6RF1

Crystal structure of the light-driven sodium pump KR2 in the pentameric "wet" form


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4XTN4XTN chain D

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1LIPIDIC CUBIC PHASE2933.4 M Sodium Malonate pH 8.0
Crystal Properties
Matthews coefficientSolvent content
3.4364.11

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 130.628α = 90
b = 240.474β = 90
c = 135.614γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 4M2017-10-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE MASSIF-30.976ESRFMASSIF-3

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
12.848.1399.60.1410.160.0720.9975.64.552539
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)
12.82.8999.41.291.4480.6450.7824.7

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 REPLACEMENTTHROUGHOUT4XTN chain D2.848.1749912262399.40.190.18830.2233RANDOM61.866
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]
9.7-8.1-1.6
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.856
r_dihedral_angle_4_deg21.151
r_dihedral_angle_3_deg16.55
r_dihedral_angle_1_deg7.844
r_angle_other_deg0.724
r_angle_refined_deg0.6
r_chiral_restr0.028
r_bond_refined_d0.003
r_gen_planes_refined0.002
r_bond_other_d
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.856
r_dihedral_angle_4_deg21.151
r_dihedral_angle_3_deg16.55
r_dihedral_angle_1_deg7.844
r_angle_other_deg0.724
r_angle_refined_deg0.6
r_chiral_restr0.028
r_bond_refined_d0.003
r_gen_planes_refined0.002
r_bond_other_d
r_gen_planes_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms10942
Nucleic Acid Atoms
Solvent Atoms199
Heterogen Atoms900

Software

Software
Software NamePurpose
Aimlessdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
MOLREPphasing