6RFB

Crystal structure of the potassium-pumping S254A mutant of the light-driven sodium pump KR2 in the monomeric form, pH 4.3


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1LIPIDIC CUBIC PHASE2932.0 M Sodium Malonate, pH 4.3
Crystal Properties
Matthews coefficientSolvent content
3.2261.78

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 40.796α = 90
b = 83β = 90
c = 234.096γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 4M2017-11-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE MASSIF-30.968ESRFMASSIF-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
12.140.7899.40.0880.10.0460.99910.94.623679
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)
12.12.161001.6741.8910.8660.534.8

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 REPLACEMENTTHROUGHOUT4XTL2.12022551109599.040.22810.22570.2794RANDOM50.253
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]
-0.476.18-5.71
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.966
r_dihedral_angle_4_deg20.547
r_dihedral_angle_3_deg16.213
r_dihedral_angle_1_deg7.768
r_angle_other_deg0.706
r_angle_refined_deg0.57
r_chiral_restr0.028
r_bond_refined_d0.003
r_gen_planes_refined0.002
r_gen_planes_other0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.966
r_dihedral_angle_4_deg20.547
r_dihedral_angle_3_deg16.213
r_dihedral_angle_1_deg7.768
r_angle_other_deg0.706
r_angle_refined_deg0.57
r_chiral_restr0.028
r_bond_refined_d0.003
r_gen_planes_refined0.002
r_gen_planes_other0.001
r_bond_other_d
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2146
Nucleic Acid Atoms
Solvent Atoms29
Heterogen Atoms292

Software

Software
Software NamePurpose
Aimlessdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
MOLREPphasing