6REZ

Crystal structure of the light-driven sodium pump KR2 in the pentameric form, pH 5.0


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4XTN4XTN chain D

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1LIPIDIC CUBIC PHASE2933.4 M Sodium Malonate pH 8.0
Crystal Properties
Matthews coefficientSolvent content
3.4264.01

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 130.241α = 90
b = 241.392β = 90
c = 135.109γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 4M2018-03-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID30B0.978ESRFID30B

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
12.648.0898.90.0870.0960.0410.9999.75.564789
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)
12.62.6699.81.7461.9240.7940.4485.7

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 REPLACEMENTTHROUGHOUT4XTN chain D2.648.1361464330198.620.19280.1910.2247RANDOM72.949
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]
5.87-5.76-0.11
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.16
r_dihedral_angle_4_deg20.643
r_dihedral_angle_3_deg17.428
r_dihedral_angle_1_deg7.456
r_angle_other_deg0.761
r_angle_refined_deg0.542
r_chiral_restr0.031
r_bond_refined_d0.002
r_gen_planes_refined0.002
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.16
r_dihedral_angle_4_deg20.643
r_dihedral_angle_3_deg17.428
r_dihedral_angle_1_deg7.456
r_angle_other_deg0.761
r_angle_refined_deg0.542
r_chiral_restr0.031
r_bond_refined_d0.002
r_gen_planes_refined0.002
r_bond_other_d0.001
r_gen_planes_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms10900
Nucleic Acid Atoms
Solvent Atoms97
Heterogen Atoms422

Software

Software
Software NamePurpose
Aimlessdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
MOLREPphasing