7ZNC

Crystal structure of the light-driven inward proton pump xenorhodopsin BcXeR in the ground state at pH 7.6 in the absence of sodium at 100K


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1XIO 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1LIPIDIC CUBIC PHASE2931.2 M Ammonium Phosphate pH 7.6
Crystal Properties
Matthews coefficientSolvent content
2.8857.29

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 68.45α = 90
b = 109.63β = 90
c = 118.46γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2020-07-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-10.972ESRFID23-1

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
11.744.7996.20.0950.9991513.382933
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.71.782.8080.4420.9

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 REPLACEMENTTHROUGHOUT1XIO1.72078775408584.020.18490.18370.2079RANDOM28.404
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]
0.350.28-0.62
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.031
r_dihedral_angle_4_deg20.76
r_dihedral_angle_3_deg13.475
r_dihedral_angle_1_deg4.748
r_angle_other_deg1.107
r_angle_refined_deg1.078
r_chiral_restr0.06
r_gen_planes_refined0.004
r_bond_refined_d0.003
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.031
r_dihedral_angle_4_deg20.76
r_dihedral_angle_3_deg13.475
r_dihedral_angle_1_deg4.748
r_angle_other_deg1.107
r_angle_refined_deg1.078
r_chiral_restr0.06
r_gen_planes_refined0.004
r_bond_refined_d0.003
r_bond_other_d0.001
r_gen_planes_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5290
Nucleic Acid Atoms
Solvent Atoms375
Heterogen Atoms812

Software

Software
Software NamePurpose
Aimlessdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
MOLREPphasing