5JRF

Crystal structure of the light-driven sodium pump KR2 bound with iodide ions


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1LIPIDIC CUBIC PHASE293in meso lipidic cubic phase crystallization
Crystal Properties
Matthews coefficientSolvent content
3.3162.86

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 40.506α = 90
b = 83.749β = 90
c = 234.102γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2015-11-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-11.85ESRFID23-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
12.356099.20.1260.99910.256.7326628
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)
12.352.595.50.9711.545.5

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DIFFRACTIONSADTHROUGHOUT2.5117.051361272099.880.19180.189780.22609RANDOM38.61
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]
0.16-0.02-0.14
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.965
r_dihedral_angle_4_deg27.203
r_dihedral_angle_3_deg14.469
r_long_range_B_refined7.099
r_long_range_B_other7.094
r_scangle_other5.739
r_dihedral_angle_1_deg5.466
r_mcangle_it4.329
r_mcangle_other4.328
r_scbond_it3.732
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.965
r_dihedral_angle_4_deg27.203
r_dihedral_angle_3_deg14.469
r_long_range_B_refined7.099
r_long_range_B_other7.094
r_scangle_other5.739
r_dihedral_angle_1_deg5.466
r_mcangle_it4.329
r_mcangle_other4.328
r_scbond_it3.732
r_scbond_other3.73
r_mcbond_it2.987
r_mcbond_other2.971
r_angle_refined_deg1.749
r_angle_other_deg1.065
r_chiral_restr0.101
r_bond_refined_d0.016
r_gen_planes_refined0.008
r_bond_other_d0.003
r_gen_planes_other0.002
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 Atoms2122
Nucleic Acid Atoms
Solvent Atoms49
Heterogen Atoms89

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
SHELXCDphasing
SHELXDEphasing