6YT4

Crystal structure of the N112A 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 6YC3 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1LIPIDIC CUBIC PHASE82931.2 M NaMal pH 8.0
Crystal Properties
Matthews coefficientSolvent content
3.2261.74

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 129.84α = 90
b = 239.7β = 90
c = 134.58γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2019-11-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06SA0.9999SLSX06SA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
12.447.85940.2160.0350.94319.640.777168
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.42.4552.7340.4360.8211.840.2

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 REPLACEMENTTHROUGHOUT6YC32.42073219376793.790.18790.18640.2168RANDOM42.133
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]
0.94-1.390.45
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.913
r_dihedral_angle_4_deg15.063
r_dihedral_angle_3_deg13.19
r_dihedral_angle_1_deg4.855
r_angle_other_deg1.084
r_angle_refined_deg1.04
r_chiral_restr0.037
r_gen_planes_refined0.003
r_bond_refined_d0.002
r_bond_other_d
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.913
r_dihedral_angle_4_deg15.063
r_dihedral_angle_3_deg13.19
r_dihedral_angle_1_deg4.855
r_angle_other_deg1.084
r_angle_refined_deg1.04
r_chiral_restr0.037
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 Atoms10796
Nucleic Acid Atoms
Solvent Atoms286
Heterogen Atoms683

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
STARANISOdata scaling
MOLREPphasing