4XTL

Crystal structure of the light-driven sodium pump KR2 in the monomeric blue form, pH 4.3


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3DDL 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1LIPIDIC CUBIC PHASE293The crystals were grown using in meso crystallization technique
Crystal Properties
Matthews coefficientSolvent content
2.957.57

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 40.18α = 90
b = 80.84β = 90
c = 232.84γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELPSI PILATUS 6M2014-07-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID290.969ESRFID29

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)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
11.4540.499.716.35.564511
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.451.599.31.3511.115.6

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 REPLACEMENTTHROUGHOUT3DDL1.4540.464511322199.660.188780.187380.21626RANDOM32.867
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]
2.70.27-2.97
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.358
r_dihedral_angle_4_deg21.059
r_dihedral_angle_3_deg12.836
r_long_range_B_refined8.677
r_long_range_B_other8.669
r_scangle_other6.873
r_scbond_it5.167
r_scbond_other5.163
r_mcangle_other4.913
r_mcangle_it4.91
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.358
r_dihedral_angle_4_deg21.059
r_dihedral_angle_3_deg12.836
r_long_range_B_refined8.677
r_long_range_B_other8.669
r_scangle_other6.873
r_scbond_it5.167
r_scbond_other5.163
r_mcangle_other4.913
r_mcangle_it4.91
r_dihedral_angle_1_deg4.222
r_mcbond_it3.864
r_mcbond_other3.861
r_angle_refined_deg1.045
r_angle_other_deg0.784
r_chiral_restr0.064
r_bond_refined_d0.007
r_gen_planes_refined0.006
r_bond_other_d0.002
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2147
Nucleic Acid Atoms
Solvent Atoms144
Heterogen Atoms292

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing