6REX

Crystal structure of the light-driven sodium pump KR2 in the pentameric form, pH 6.0


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4XTN 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1LIPIDIC CUBIC PHASE2933.4 M Sodium Malonate pH 6.0
Crystal Properties
Matthews coefficientSolvent content
3.4664.41

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 131.432α = 90
b = 240.787β = 90
c = 135.737γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2016-06-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-11.000ESRFID23-1

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
12.748.2196.90.190.2120.0910.9917.94.857277
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)
12.72.7798.61.3081.4580.6270.6324.7

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 REPLACEMENTTHROUGHOUT4XTN2.748.2654451280396.470.22420.22290.2503RANDOM39.003
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]
3.82-4.670.84
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.859
r_dihedral_angle_4_deg22.495
r_dihedral_angle_3_deg16.338
r_dihedral_angle_1_deg7.608
r_angle_other_deg0.72
r_angle_refined_deg0.56
r_chiral_restr0.029
r_bond_refined_d0.002
r_bond_other_d0.002
r_gen_planes_refined0.002
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.859
r_dihedral_angle_4_deg22.495
r_dihedral_angle_3_deg16.338
r_dihedral_angle_1_deg7.608
r_angle_other_deg0.72
r_angle_refined_deg0.56
r_chiral_restr0.029
r_bond_refined_d0.002
r_bond_other_d0.002
r_gen_planes_refined0.002
r_gen_planes_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms10942
Nucleic Acid Atoms
Solvent Atoms316
Heterogen Atoms904

Software

Software
Software NamePurpose
Aimlessdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
MOLREPphasing