6S63

Dark-adapted structure of Archaerhodopsin-3 obtained from LCP crystals using a thin-film sandwich at room temperature


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1LIPIDIC CUBIC PHASE5.5293100mM MES pH 5.5, 33% PEG 600, 150mM Na chloride, 150mM Ca chloride
Crystal Properties
Matthews coefficientSolvent content
2.2444.97

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 45.91α = 90
b = 48.351β = 90
c = 105.364γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray293PIXELDECTRIS PILATUS3 6M2017-03-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I240.96862DiamondI24

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
11.85105.3688.990.4010.1260.9956.68.518417
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.851.8888.130.1380.6230.3161.3

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 REPLACEMENTTHROUGHOUT1UAZ1.8552.681748597089.180.17560.17470.1917RANDOM26.542
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]
1.23-0.14-1.09
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.806
r_dihedral_angle_4_deg23.89
r_dihedral_angle_3_deg12.378
r_dihedral_angle_1_deg4.569
r_angle_refined_deg0.951
r_angle_other_deg0.337
r_chiral_restr0.058
r_bond_refined_d0.004
r_gen_planes_refined0.004
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.806
r_dihedral_angle_4_deg23.89
r_dihedral_angle_3_deg12.378
r_dihedral_angle_1_deg4.569
r_angle_refined_deg0.951
r_angle_other_deg0.337
r_chiral_restr0.058
r_bond_refined_d0.004
r_gen_planes_refined0.004
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1814
Nucleic Acid Atoms
Solvent Atoms75
Heterogen Atoms435

Software

Software
Software NamePurpose
REFMACrefinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
PDB_EXTRACTdata extraction