6YBZ

Crystal structure of the D116N 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 4XTO 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1LIPIDIC CUBIC PHASE82931.2 M NaMal pH 8.0
Crystal Properties
Matthews coefficientSolvent content
3.4764.56

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 131.343α = 90
b = 240.477β = 90
c = 135.415γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2018-07-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID290.978ESRFID29

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
12.3548.1399.90.110.1190.0450.99911.36.989161
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)
12.352.3999.91.9252.090.8080.7876.6

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 REPLACEMENTTHROUGHOUT4xto2.352084508445999.730.19720.19610.2175RANDOM32.34
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]
4.27-7.042.76
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.689
r_dihedral_angle_4_deg20.388
r_dihedral_angle_3_deg17.799
r_dihedral_angle_1_deg6.586
r_angle_other_deg2.375
r_angle_refined_deg1.088
r_chiral_restr0.043
r_bond_other_d0.034
r_bond_refined_d0.01
r_gen_planes_refined0.004
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.689
r_dihedral_angle_4_deg20.388
r_dihedral_angle_3_deg17.799
r_dihedral_angle_1_deg6.586
r_angle_other_deg2.375
r_angle_refined_deg1.088
r_chiral_restr0.043
r_bond_other_d0.034
r_bond_refined_d0.01
r_gen_planes_refined0.004
r_gen_planes_other0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms10737
Nucleic Acid Atoms
Solvent Atoms175
Heterogen Atoms445

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
MOLREPphasing