4XTN

Crystal structure of the light-driven sodium pump KR2 in the pentameric red form, pH 4.9


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1LIPIDIC CUBIC PHASE293The crystals were grown using in meso crystallization technique
Crystal Properties
Matthews coefficientSolvent content
3.261.57

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 81.69α = 90
b = 107β = 90.11
c = 240.8γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELPSI PILATUS 6M2014-05-21MSINGLE 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
12.248.996.272.8192342
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)
2.22.2897.80.9751.22.8

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 REPLACEMENTTHROUGHOUT4XTL2.248.9192342979796.160.19680.194820.236RANDOM35.945
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]
1.39-0.191.74-3.13
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.781
r_dihedral_angle_4_deg14.07
r_dihedral_angle_3_deg12.982
r_long_range_B_refined7.015
r_long_range_B_other7.015
r_scangle_other5.837
r_mcangle_it4.42
r_mcangle_other4.42
r_dihedral_angle_1_deg4.231
r_scbond_it4.144
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.781
r_dihedral_angle_4_deg14.07
r_dihedral_angle_3_deg12.982
r_long_range_B_refined7.015
r_long_range_B_other7.015
r_scangle_other5.837
r_mcangle_it4.42
r_mcangle_other4.42
r_dihedral_angle_1_deg4.231
r_scbond_it4.144
r_scbond_other4.144
r_mcbond_it3.329
r_mcbond_other3.328
r_angle_other_deg1.121
r_angle_refined_deg0.832
r_chiral_restr0.049
r_bond_refined_d0.004
r_bond_other_d0.003
r_gen_planes_refined0.003
r_gen_planes_other0.001
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 Atoms21636
Nucleic Acid Atoms
Solvent Atoms351
Heterogen Atoms1324

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing