6RF6

Crystal structure of the light-driven sodium pump KR2 in the monomeric form, pH 8.0


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4XTL 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1LIPIDIC CUBIC PHASE2932.0 M Sodium Malonate, pH 4.3
Crystal Properties
Matthews coefficientSolvent content
3.1661.13

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 40.411α = 90
b = 82.319β = 90
c = 233.35γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2018-03-11MSINGLE 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
11.840.699.90.0390.0440.0190.99919.15.236723
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)
11.81.8499.90.4280.4740.2010.9255.4

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 REPLACEMENTTHROUGHOUT4XTL1.82035277141699.640.1440.14250.1807RANDOM37.42
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]
1.460.9-2.36
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free39.61
r_dihedral_angle_2_deg36.148
r_sphericity_bonded21.219
r_dihedral_angle_4_deg17.847
r_dihedral_angle_3_deg12.543
r_rigid_bond_restr6.208
r_dihedral_angle_1_deg5.668
r_angle_other_deg0.902
r_angle_refined_deg0.767
r_chiral_restr0.053
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free39.61
r_dihedral_angle_2_deg36.148
r_sphericity_bonded21.219
r_dihedral_angle_4_deg17.847
r_dihedral_angle_3_deg12.543
r_rigid_bond_restr6.208
r_dihedral_angle_1_deg5.668
r_angle_other_deg0.902
r_angle_refined_deg0.767
r_chiral_restr0.053
r_bond_refined_d0.004
r_gen_planes_refined0.004
r_gen_planes_other0.001
r_bond_other_d
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2136
Nucleic Acid Atoms
Solvent Atoms93
Heterogen Atoms186

Software

Software
Software NamePurpose
Aimlessdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
MOLREPphasing