7CLJ

Crystal structure of Thermoplasmatales archaeon heliorhodopsin E108D mutant


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6IS6 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1LIPIDIC CUBIC PHASE529325% PEG 350 MME, 100mM Na-citrate, 100mM ammonium sulfate or lithium sulfate
Crystal Properties
Matthews coefficientSolvent content
2.5651.87

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 72.86α = 90
b = 72.86β = 90
c = 115.05γ = 90
Symmetry
Space GroupP 42 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 9M2019-11-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL32XU1.000SPring-8BL32XU

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
12.63099.10.380.9825.367.719975
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)
12.62.7698.61.8060.4841.047.6

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE6is62.628.368997550299.0960.2250.22150.283436.753
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]
-0.017-0.0170.033
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.561
r_dihedral_angle_3_deg18.287
r_dihedral_angle_4_deg15.758
r_lrange_it6.992
r_lrange_other6.991
r_dihedral_angle_1_deg5.284
r_scangle_it3.25
r_scangle_other3.249
r_mcangle_it3.158
r_mcangle_other3.156
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.561
r_dihedral_angle_3_deg18.287
r_dihedral_angle_4_deg15.758
r_lrange_it6.992
r_lrange_other6.991
r_dihedral_angle_1_deg5.284
r_scangle_it3.25
r_scangle_other3.249
r_mcangle_it3.158
r_mcangle_other3.156
r_scbond_it1.988
r_scbond_other1.987
r_mcbond_other1.885
r_mcbond_it1.884
r_angle_refined_deg1.359
r_angle_other_deg1.166
r_symmetry_xyhbond_nbd_refined0.435
r_symmetry_nbd_refined0.249
r_nbd_refined0.188
r_xyhbond_nbd_refined0.179
r_nbtor_refined0.175
r_symmetry_nbd_other0.174
r_nbd_other0.173
r_symmetry_nbtor_other0.078
r_chiral_restr0.065
r_bond_refined_d0.005
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2007
Nucleic Acid Atoms
Solvent Atoms15
Heterogen Atoms250

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing