4XXJ

Crystal Structure of Escherichia coli-Expressed Halobacterium salinarum Bacteriorhodopsin in the Trimeric Form


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1C3W 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1LIPIDIC CUBIC PHASE293The crystals were grown using in meso crystallization technique
Crystal Properties
Matthews coefficientSolvent content
2.0439.59

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 105.84α = 90
b = 60.76β = 99.78
c = 113.36γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELPSI PILATUS 6M2013-11-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-10.976ESRFID23-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
11.949.298.80.07113.74.556113
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)
11.91.9598.31.1021.414.5

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 REPLACEMENTTHROUGHOUT1C3W1.949.252689277098.830.185020.183450.2139RANDOM33.762
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]
0.790.01-1.030.22
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.323
r_dihedral_angle_3_deg14.017
r_dihedral_angle_4_deg13.98
r_long_range_B_refined7.71
r_long_range_B_other7.71
r_scangle_other6.235
r_mcangle_other4.557
r_scbond_it4.557
r_scbond_other4.556
r_mcangle_it4.554
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.323
r_dihedral_angle_3_deg14.017
r_dihedral_angle_4_deg13.98
r_long_range_B_refined7.71
r_long_range_B_other7.71
r_scangle_other6.235
r_mcangle_other4.557
r_scbond_it4.557
r_scbond_other4.556
r_mcangle_it4.554
r_dihedral_angle_1_deg3.949
r_mcbond_other3.529
r_mcbond_it3.528
r_angle_other_deg1.327
r_angle_refined_deg0.938
r_chiral_restr0.054
r_bond_refined_d0.005
r_gen_planes_refined0.005
r_bond_other_d0.001
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 Atoms5279
Nucleic Acid Atoms
Solvent Atoms90
Heterogen Atoms320

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing