8R98

Crystal structure of the cryorhodopsin CryoR2 at pH 4.6, type B crystals, illuminated state


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelOthermodel from cryo-EM data

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1LIPIDIC CUBIC PHASE4.62931.2M Na/K-Pi pH 4.6
Crystal Properties
Matthews coefficientSolvent content
2.6753.89

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 150.108α = 90
b = 84.964β = 96.87
c = 296.943γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 X 16M2023-03-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPETRA III, EMBL c/o DESY BEAMLINE P14 (MX2)0.9763PETRA III, EMBL c/o DESYP14 (MX2)

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.77474.38763.340.0850.99876.5126.8859820
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.7743.11.0610.3825

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT32054950285077.20.288140.287010.30938RANDOM84.75
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]
1.9-0.080.95-2.74
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg18.35
r_dihedral_angle_3_deg9.979
r_scangle_other8.941
r_mcangle_it8.871
r_mcangle_other8.871
r_dihedral_angle_4_deg8.489
r_mcbond_it5.485
r_mcbond_other5.484
r_scbond_it5.435
r_scbond_other5.427
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg18.35
r_dihedral_angle_3_deg9.979
r_scangle_other8.941
r_mcangle_it8.871
r_mcangle_other8.871
r_dihedral_angle_4_deg8.489
r_mcbond_it5.485
r_mcbond_other5.484
r_scbond_it5.435
r_scbond_other5.427
r_dihedral_angle_1_deg2.658
r_angle_other_deg1.137
r_angle_refined_deg1.07
r_chiral_restr0.032
r_bond_other_d0.004
r_bond_refined_d0.002
r_gen_planes_refined0.002
r_gen_planes_other0.001
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 Atoms21522
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms326

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
STARANISOdata scaling
MOLREPphasing