6XYT

Crystal structure of the O-state 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 PHASE2930.7 M Sodium Malonate pH 8.0
Crystal Properties
Matthews coefficientSolvent content
3.4364.13

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 131.157α = 90
b = 240.629β = 90
c = 135.039γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2019-05-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPETRA III, EMBL c/o DESY BEAMLINE P14 (MX2)1.00PETRA III, EMBL c/o DESYP14 (MX2)

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
12.148.0699.80.0780.0810.0220.99920.113.8123865
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)
12.12.1499.92.762.8630.7570.5614

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 REPLACEMENTTHROUGHOUT6REW2.120117421623499.580.17980.17890.1974RANDOM57.586
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]
5-5.510.51
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.934
r_dihedral_angle_4_deg14.291
r_dihedral_angle_3_deg13.024
r_dihedral_angle_1_deg4.933
r_angle_other_deg1.108
r_angle_refined_deg1.052
r_chiral_restr0.044
r_bond_refined_d0.003
r_gen_planes_refined0.003
r_bond_other_d
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.934
r_dihedral_angle_4_deg14.291
r_dihedral_angle_3_deg13.024
r_dihedral_angle_1_deg4.933
r_angle_other_deg1.108
r_angle_refined_deg1.052
r_chiral_restr0.044
r_bond_refined_d0.003
r_gen_planes_refined0.003
r_bond_other_d
r_gen_planes_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms10865
Nucleic Acid Atoms
Solvent Atoms299
Heterogen Atoms1185

Software

Software
Software NamePurpose
Aimlessdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
MOLREPphasing