8QLF

Crystal structure of the light-driven sodium pump ErNaR in the monomeric form at pH 8.8


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1LIPIDIC CUBIC PHASE8.82930.1M sodium acetate, 10% PEG550MME, soaked in 0.1M Tris-HCl pH 8.8, 10% PEG550MME prior to crystal harvesting.
Crystal Properties
Matthews coefficientSolvent content
2.3447.51

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 53.382α = 90
b = 53.382β = 90
c = 364.842γ = 120
Symmetry
Space GroupP 61 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2022-02-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPETRA III, EMBL c/o DESY BEAMLINE P14 (MX2)0.976PETRA III, EMBL c/o DESYP14 (MX2)

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)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
11.70746.2394.660.0380.999113.76937.626414
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.7071.8750.5180.74441.59

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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1.712025066130475.490.184430.182710.21819RANDOM29.838
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]
0.270.140.27-0.89
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.68
r_dihedral_angle_3_deg13.515
r_dihedral_angle_4_deg13.013
r_long_range_B_other6.728
r_long_range_B_refined6.722
r_scangle_other5.449
r_dihedral_angle_1_deg5.135
r_mcangle_other3.808
r_mcangle_it3.804
r_scbond_other3.681
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.68
r_dihedral_angle_3_deg13.515
r_dihedral_angle_4_deg13.013
r_long_range_B_other6.728
r_long_range_B_refined6.722
r_scangle_other5.449
r_dihedral_angle_1_deg5.135
r_mcangle_other3.808
r_mcangle_it3.804
r_scbond_other3.681
r_scbond_it3.676
r_mcbond_it2.828
r_mcbond_other2.812
r_angle_other_deg1.113
r_angle_refined_deg1.046
r_chiral_restr0.049
r_bond_refined_d0.003
r_gen_planes_refined0.003
r_gen_planes_other0.001
r_bond_other_d
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 Atoms2168
Nucleic Acid Atoms
Solvent Atoms112
Heterogen Atoms214

Software

Software
Software NamePurpose
REFMACrefinement
MOLREPphasing
XDSdata reduction
STARANISOdata scaling