6RF0

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


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1LIPIDIC CUBIC PHASE2933.4 M Sodium Malonate pH 8.0
Crystal Properties
Matthews coefficientSolvent content
3.2762.36

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 128.184α = 90
b = 239.719β = 90
c = 131.909γ = 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 ID30B0.976ESRFID30B

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
1347.2899.90.3040.330.1270.9895.76.641018
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)
133.121001.4751.6010.6180.6626.6

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 REPLACEMENTTHROUGHOUT4XTO347.3238937205999.920.21840.21660.2519RANDOM43.925
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]
5.3-6.491.19
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.261
r_dihedral_angle_4_deg26.713
r_dihedral_angle_3_deg19.243
r_dihedral_angle_1_deg7.637
r_angle_other_deg0.766
r_angle_refined_deg0.59
r_chiral_restr0.028
r_bond_refined_d0.003
r_gen_planes_refined0.002
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.261
r_dihedral_angle_4_deg26.713
r_dihedral_angle_3_deg19.243
r_dihedral_angle_1_deg7.637
r_angle_other_deg0.766
r_angle_refined_deg0.59
r_chiral_restr0.028
r_bond_refined_d0.003
r_gen_planes_refined0.002
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms10841
Nucleic Acid Atoms
Solvent Atoms41
Heterogen Atoms206

Software

Software
Software NamePurpose
Aimlessdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
MOLREPphasing