8QLE

Crystal structure of the light-driven sodium pump ErNaR in the monomeric form at pH 4.6


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1LIPIDIC CUBIC PHASE4.62930.1M sodium acetate pH 4.6, 10% PEG 550MME.
Crystal Properties
Matthews coefficientSolvent content
2.3547.58

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 53.401α = 90
b = 53.401β = 90
c = 365.052γ = 120
Symmetry
Space GroupP 61 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2021-03-29MSINGLE 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
11.66460.84294.20.0520.998711.03835.930115
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)
11.6641.76378.41.1610.35740.698

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 REPLACEMENTTHROUGHOUT1.72028309146883.40.213540.211780.24781RANDOM29.044
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]
0.260.130.26-0.83
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.926
r_dihedral_angle_4_deg14.674
r_dihedral_angle_3_deg13.87
r_long_range_B_other6.41
r_long_range_B_refined6.407
r_scangle_other5.124
r_dihedral_angle_1_deg5.042
r_scbond_other3.573
r_scbond_it3.572
r_mcangle_it3.571
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.926
r_dihedral_angle_4_deg14.674
r_dihedral_angle_3_deg13.87
r_long_range_B_other6.41
r_long_range_B_refined6.407
r_scangle_other5.124
r_dihedral_angle_1_deg5.042
r_scbond_other3.573
r_scbond_it3.572
r_mcangle_it3.571
r_mcangle_other3.571
r_mcbond_it2.748
r_mcbond_other2.742
r_angle_other_deg1.138
r_angle_refined_deg1.025
r_chiral_restr0.046
r_gen_planes_refined0.003
r_bond_refined_d0.002
r_bond_other_d
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 Atoms2168
Nucleic Acid Atoms
Solvent Atoms87
Heterogen Atoms147

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
STARANISOdata scaling
MOLREPphasing