6RF5

Crystal structure of the light-driven sodium pump KR2 in the monomeric form, pH 6.0


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
3.1260.58

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 40.334α = 90
b = 81.246β = 90
c = 233.359γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2016-06-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-11.000ESRFID23-1

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
12.340.6299.70.1050.1160.0490.99710.45.417576
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)
12.32.3999.51.0581.1770.5060.6835.2

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 REPLACEMENTTHROUGHOUT4XTL2.3201671183199.310.20470.2020.2585RANDOM43.942
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]
4.530.14-4.66
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.858
r_dihedral_angle_4_deg20.175
r_dihedral_angle_3_deg15.641
r_dihedral_angle_1_deg7.085
r_angle_other_deg0.725
r_angle_refined_deg0.584
r_chiral_restr0.034
r_bond_refined_d0.003
r_gen_planes_refined0.002
r_gen_planes_other0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.858
r_dihedral_angle_4_deg20.175
r_dihedral_angle_3_deg15.641
r_dihedral_angle_1_deg7.085
r_angle_other_deg0.725
r_angle_refined_deg0.584
r_chiral_restr0.034
r_bond_refined_d0.003
r_gen_planes_refined0.002
r_gen_planes_other0.001
r_bond_other_d
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2134
Nucleic Acid Atoms
Solvent Atoms47
Heterogen Atoms276

Software

Software
Software NamePurpose
Aimlessdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
MOLREPphasing