7Q37

Crystal structure of proton pump MAR rhodopsin pressurized with krypton


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5JSI 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1LIPIDIC CUBIC PHASE2932.6 M ammonium sulfate, 0.1 M sodium acetate, pH 5.2
Crystal Properties
Matthews coefficientSolvent content
2.5151.05

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 50.897α = 90
b = 40.381β = 101.36
c = 60.619γ = 90
Symmetry
Space GroupP 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2018-11-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID290.861ESRFID29

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Rrim 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
12.2510099.40.140.9967.743.522357
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rrim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.252.3597.91.2990.4911.143.5

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 REPLACEMENTTHROUGHOUT5JSI2.2559.431110257099.740.181170.177850.24468RANDOM34.645
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]
0.1-1.12-1.571.77
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.926
r_dihedral_angle_4_deg19.738
r_dihedral_angle_3_deg14.624
r_long_range_B_refined7.114
r_long_range_B_other6.989
r_dihedral_angle_1_deg5.69
r_scangle_other5.33
r_mcangle_other3.604
r_mcangle_it3.599
r_scbond_it3.527
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.926
r_dihedral_angle_4_deg19.738
r_dihedral_angle_3_deg14.624
r_long_range_B_refined7.114
r_long_range_B_other6.989
r_dihedral_angle_1_deg5.69
r_scangle_other5.33
r_mcangle_other3.604
r_mcangle_it3.599
r_scbond_it3.527
r_scbond_other3.525
r_mcbond_it2.55
r_mcbond_other2.52
r_angle_refined_deg1.457
r_angle_other_deg1.288
r_chiral_restr0.075
r_bond_refined_d0.01
r_gen_planes_refined0.008
r_bond_other_d0.002
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 Atoms1676
Nucleic Acid Atoms
Solvent Atoms99
Heterogen Atoms201

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing