7Q38

Crystal structure of the mutant bacteriorhodopsin pressurized with argon


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
2.1643.06

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 115.657α = 90
b = 119.245β = 90
c = 36.393γ = 90
Symmetry
Space GroupC 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2018-09-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-10.97241ESRFID23-1

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
11.65100990.050.99916.293.157738
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)
11.651.799.41.7690.340.923.1

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 REPLACEMENTTHROUGHOUT4XXJ1.6583.0229182156999.620.164520.162320.20522RANDOM27.514
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]
-0.08-0.670.75
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.406
r_dihedral_angle_4_deg17.897
r_dihedral_angle_3_deg12.033
r_long_range_B_other7.134
r_long_range_B_refined7.132
r_scangle_other5.095
r_dihedral_angle_1_deg5.014
r_scbond_it3.639
r_scbond_other3.511
r_mcangle_other3.046
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.406
r_dihedral_angle_4_deg17.897
r_dihedral_angle_3_deg12.033
r_long_range_B_other7.134
r_long_range_B_refined7.132
r_scangle_other5.095
r_dihedral_angle_1_deg5.014
r_scbond_it3.639
r_scbond_other3.511
r_mcangle_other3.046
r_mcangle_it3.041
r_mcbond_it2.077
r_mcbond_other2.048
r_angle_refined_deg1.81
r_angle_other_deg1.421
r_chiral_restr0.107
r_bond_refined_d0.013
r_gen_planes_refined0.01
r_bond_other_d0.002
r_gen_planes_other0.002
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 Atoms1737
Nucleic Acid Atoms
Solvent Atoms119
Heterogen Atoms296

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing