6YC3

Crystal structure 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 PHASE82931.2 M NaMal pH 8.0
Crystal Properties
Matthews coefficientSolvent content
3.4864.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 131.866α = 90
b = 240.323β = 90
c = 135.513γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2019-10-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPETRA III, EMBL c/o DESY BEAMLINE P14 (MX2)0.976PETRA III, EMBL c/o DESYP14 (MX2)

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
1248.1699.90.0760.0820.030.99913.27.6144508
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)
122.031001.7491.8760.6740.7437.7

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 REPLACEMENTTHROUGHOUT6rew220137104720999.780.16970.16830.1953RANDOM47.553
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]
5.42-5.420.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.884
r_dihedral_angle_4_deg15.18
r_dihedral_angle_3_deg13.017
r_dihedral_angle_1_deg5.301
r_angle_other_deg1.139
r_angle_refined_deg1.071
r_chiral_restr0.05
r_gen_planes_refined0.004
r_bond_refined_d0.003
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.884
r_dihedral_angle_4_deg15.18
r_dihedral_angle_3_deg13.017
r_dihedral_angle_1_deg5.301
r_angle_other_deg1.139
r_angle_refined_deg1.071
r_chiral_restr0.05
r_gen_planes_refined0.004
r_bond_refined_d0.003
r_bond_other_d0.001
r_gen_planes_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms10828
Nucleic Acid Atoms
Solvent Atoms607
Heterogen Atoms1320

Software

Software
Software NamePurpose
Aimlessdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
MOLREPphasing