7AKY

Crystal structure of the viral rhodopsin OLPVR1 in P21212 space group


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6SQG 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1LIPIDIC CUBIC PHASE8.229310 mM CaCl2, 10 mM MgCl2, 24% PEG 6000, 100mM Tris (pH 8.2), monopalmitolein
Crystal Properties
Matthews coefficientSolvent content
2.6453.46

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 46.525α = 90
b = 115.796β = 90
c = 53.529γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2018-06-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID30B0.97625ESRFID30B

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)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
11.448.591000.0720.0780.0310.99812.36.357845
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.41.4299.91.811.9720.7750.4536.3

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 REPLACEMENTTHROUGHOUT6sqg1.42054864289699.870.14510.14270.1879RANDOM24.189
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]
-0.390.89-0.5
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.743
r_dihedral_angle_4_deg23.378
r_dihedral_angle_3_deg16.011
r_rigid_bond_restr10.934
r_dihedral_angle_1_deg6.665
r_angle_other_deg1.388
r_angle_refined_deg1.048
r_chiral_restr0.065
r_gen_planes_refined0.01
r_bond_refined_d0.004
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.743
r_dihedral_angle_4_deg23.378
r_dihedral_angle_3_deg16.011
r_rigid_bond_restr10.934
r_dihedral_angle_1_deg6.665
r_angle_other_deg1.388
r_angle_refined_deg1.048
r_chiral_restr0.065
r_gen_planes_refined0.01
r_bond_refined_d0.004
r_bond_other_d0.003
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1920
Nucleic Acid Atoms
Solvent Atoms107
Heterogen Atoms219

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
MOLREPphasing