4X32

Bacteriorhodopsin ground state structure collected in cryo conditions from crystals obtained in LCP with PEG as a precipitant.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2NTU 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1LIPIDIC CUBIC PHASE5.629427% PEG2000, 100 mM phosphate buffer pH 5.6
Crystal Properties
Matthews coefficientSolvent content
2.1542.71

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 60.525α = 90
b = 60.525β = 90
c = 101.48γ = 120
Symmetry
Space GroupP 63

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELPSI PILATUS 6M2014-02-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06SA1.0SLSX06SA

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
11.946.571000.0950.026117.914.1166471664333.4
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)
11.91.941001.8670.4960.5481.814.31072

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 REPLACEMENTTHROUGHOUT2NTU1.952.421577384199.980.17370.17150.2143RANDOM36.741
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]
-1.03-0.51-1.033.33
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.888
r_dihedral_angle_3_deg12.706
r_dihedral_angle_4_deg11.915
r_dihedral_angle_1_deg4.646
r_mcangle_it1.92
r_mcbond_other1.349
r_mcbond_it1.348
r_angle_refined_deg1.223
r_angle_other_deg0.768
r_chiral_restr0.072
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.888
r_dihedral_angle_3_deg12.706
r_dihedral_angle_4_deg11.915
r_dihedral_angle_1_deg4.646
r_mcangle_it1.92
r_mcbond_other1.349
r_mcbond_it1.348
r_angle_refined_deg1.223
r_angle_other_deg0.768
r_chiral_restr0.072
r_bond_refined_d0.009
r_gen_planes_refined0.009
r_bond_other_d0.002
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1710
Nucleic Acid Atoms
Solvent Atoms30
Heterogen Atoms124

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PDB_EXTRACTdata extraction
PHASERphasing