7ZSI

Structure of Orange Carotenoid Protein with canthaxanthin bound after 5 minutes of illumination


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4XB5 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP4.5293100 mM sodium acetate pH 4.5, 10 % poly-ethylene glycol 20,000, 3 % glycerol
Crystal Properties
Matthews coefficientSolvent content
2.5351.41

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 82.78α = 90
b = 82.78β = 90
c = 87.604γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 XE 16M2019-07-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.9795DiamondI03

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)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
11.39955.5421000.1330.140.04414.419.868765
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.41.449.911.513.645

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 REPLACEMENTTHROUGHOUT4XB51.39955.54268710341099.8970.1920.19120.204825.71
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]
0.0090.0040.009-0.029
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.548
r_dihedral_angle_4_deg20.007
r_dihedral_angle_3_deg13.19
r_lrange_it7.245
r_dihedral_angle_1_deg5.821
r_scangle_it4.051
r_mcangle_it3.099
r_scbond_it2.774
r_mcbond_it2.072
r_angle_refined_deg1.738
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.548
r_dihedral_angle_4_deg20.007
r_dihedral_angle_3_deg13.19
r_lrange_it7.245
r_dihedral_angle_1_deg5.821
r_scangle_it4.051
r_mcangle_it3.099
r_scbond_it2.774
r_mcbond_it2.072
r_angle_refined_deg1.738
r_symmetry_xyhbond_nbd_refined0.365
r_nbtor_refined0.311
r_xyhbond_nbd_refined0.269
r_symmetry_nbd_refined0.229
r_nbd_refined0.212
r_chiral_restr0.104
r_bond_refined_d0.011
r_gen_planes_refined0.011
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2411
Nucleic Acid Atoms
Solvent Atoms400
Heterogen Atoms53

Software

Software
Software NamePurpose
REFMACrefinement
DIALSdata reduction
DIALSdata scaling
MOLREPphasing