7Q36

Crystal structure of KR2 sodium pump rhodopsin pressurized with krypton


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4XTL 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1LIPIDIC CUBIC PHASE2932.0 M sodium malonate, pH 4.3
Crystal Properties
Matthews coefficientSolvent content
3.0559.71

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 40.489α = 90
b = 82.18β = 90
c = 233.442γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2018-09-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-10.8637ESRFID23-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
12.6116.7299.90.1770.1920.9989.296.9232741
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.62.810022.1170.47

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 REPLACEMENTTHROUGHOUT4XTL2.6116.721189660799.820.219020.216470.26904RANDOM46.83
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]
3.92-0.23-3.69
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.363
r_dihedral_angle_4_deg19.913
r_dihedral_angle_3_deg13.588
r_long_range_B_refined6.137
r_long_range_B_other6.136
r_dihedral_angle_1_deg5.236
r_scangle_other3.468
r_mcangle_it3.149
r_mcangle_other3.148
r_scbond_it2.042
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.363
r_dihedral_angle_4_deg19.913
r_dihedral_angle_3_deg13.588
r_long_range_B_refined6.137
r_long_range_B_other6.136
r_dihedral_angle_1_deg5.236
r_scangle_other3.468
r_mcangle_it3.149
r_mcangle_other3.148
r_scbond_it2.042
r_scbond_other2.042
r_mcbond_it1.94
r_mcbond_other1.936
r_angle_refined_deg1.14
r_angle_other_deg1.069
r_chiral_restr0.047
r_bond_refined_d0.003
r_gen_planes_refined0.003
r_bond_other_d0.001
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 Atoms2157
Nucleic Acid Atoms
Solvent Atoms81
Heterogen Atoms206

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing