6YC1

Crystal structure of the H30A mutant 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
3.4564.39

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 131.089α = 90
b = 239.733β = 90
c = 135.132γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 S 6M2018-08-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID30B0.987ESRFID30B

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
12.248.0198.90.1220.1320.0490.99911.57.1106450
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)
12.22.2499.22.0992.2590.8270.4897.4

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 REPLACEMENTTHROUGHOUT6rew2.220100998526798.650.18270.18140.2089RANDOM47.815
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]
4.77-4.48-0.29
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.732
r_dihedral_angle_4_deg15.359
r_dihedral_angle_3_deg13.496
r_dihedral_angle_1_deg5.306
r_angle_other_deg1.068
r_angle_refined_deg1.048
r_chiral_restr0.041
r_gen_planes_refined0.003
r_bond_refined_d0.002
r_bond_other_d
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.732
r_dihedral_angle_4_deg15.359
r_dihedral_angle_3_deg13.496
r_dihedral_angle_1_deg5.306
r_angle_other_deg1.068
r_angle_refined_deg1.048
r_chiral_restr0.041
r_gen_planes_refined0.003
r_bond_refined_d0.002
r_bond_other_d
r_gen_planes_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms10911
Nucleic Acid Atoms
Solvent Atoms567
Heterogen Atoms1215

Software

Software
Software NamePurpose
Aimlessdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
MOLREPphasing