7Q35

Crystal structure of the mutant bacteriorhodopsin pressurized with krypton


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1LIPIDIC CUBIC PHASE2933.0 M Ammonium Sulfate,0.1 M Sodium Acetate, pH 4.6
Crystal Properties
Matthews coefficientSolvent content
2.1743.35

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 115.33α = 90
b = 119.986β = 90
c = 36.461γ = 90
Symmetry
Space GroupC 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2018-09-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-10.8634ESRFID23-1

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
126099.70.1420.1490.9989.096.733739
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)
122.199.81.860.5171.496.7

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 REPLACEMENTTHROUGHOUT4XXJ241.611676483899.750.172380.169490.23199RANDOM29.375
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]
-0.06-1.731.79
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.814
r_dihedral_angle_4_deg21.316
r_dihedral_angle_3_deg12.823
r_long_range_B_refined6.677
r_long_range_B_other6.676
r_dihedral_angle_1_deg4.726
r_scangle_other4.686
r_scbond_it3.167
r_scbond_other3.162
r_mcangle_other2.875
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.814
r_dihedral_angle_4_deg21.316
r_dihedral_angle_3_deg12.823
r_long_range_B_refined6.677
r_long_range_B_other6.676
r_dihedral_angle_1_deg4.726
r_scangle_other4.686
r_scbond_it3.167
r_scbond_other3.162
r_mcangle_other2.875
r_mcangle_it2.869
r_mcbond_it2.003
r_mcbond_other1.964
r_angle_refined_deg1.489
r_angle_other_deg1.313
r_chiral_restr0.083
r_bond_refined_d0.01
r_gen_planes_refined0.008
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 Atoms1706
Nucleic Acid Atoms
Solvent Atoms106
Heterogen Atoms266

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing