3WQJ

Crystal structure of archaerhodopsin-2 at 1.8 angstrom resolution


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2EI4PDB ENTRY 2EI4

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP72832.8M AMMONIUM SULFATE, 0.1M HEPES, 0.32% NONYLGLUCOSIDE, 8% trehalose, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 283K
Crystal Properties
Matthews coefficientSolvent content
2.2545.23

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 62.739α = 90
b = 62.739β = 90
c = 331.464γ = 120
Symmetry
Space GroupH 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2013-01-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL38B11.0SPring-8BL38B1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
11.845.1191.30.0540.05428.58.824035219442.12.123.15
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.81.91000.50.55.193460

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 REPLACEMENTTHROUGHOUTPDB ENTRY 2EI41.81521701110590.520.21270.21120.241RANDOM26.661
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]
0.940.470.94-1.41
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.439
r_dihedral_angle_4_deg19.248
r_dihedral_angle_3_deg17.503
r_dihedral_angle_1_deg4.917
r_scangle_it4.205
r_scbond_it2.729
r_angle_refined_deg2.033
r_mcangle_it1.704
r_mcbond_it0.983
r_chiral_restr0.221
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.439
r_dihedral_angle_4_deg19.248
r_dihedral_angle_3_deg17.503
r_dihedral_angle_1_deg4.917
r_scangle_it4.205
r_scbond_it2.729
r_angle_refined_deg2.033
r_mcangle_it1.704
r_mcbond_it0.983
r_chiral_restr0.221
r_bond_refined_d0.018
r_gen_planes_refined0.01
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1810
Nucleic Acid Atoms
Solvent Atoms51
Heterogen Atoms180

Software

Software
Software NamePurpose
ADSCdata collection
CNSrefinement
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
CNSphasing