7ZSJ

Structure of Orange Carotenoid Protein with canthaxanthin bound after 10 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
2.4750.26

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 82.26α = 90
b = 82.26β = 90
c = 86.25γ = 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
11.3729.861000.0460.0480.01524.619.271802
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)
11.371.412.5612.740.966

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 REPLACEMENTTHROUGHOUT4XB51.4128.76765306320799.8840.1930.19080.230131.033
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]
0.0680.0340.068-0.22
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.192
r_dihedral_angle_4_deg18.319
r_dihedral_angle_3_deg13.493
r_lrange_it7.545
r_dihedral_angle_1_deg6.883
r_scangle_it3.987
r_mcangle_it3.092
r_scbond_it2.847
r_mcbond_it2.13
r_angle_refined_deg1.767
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.192
r_dihedral_angle_4_deg18.319
r_dihedral_angle_3_deg13.493
r_lrange_it7.545
r_dihedral_angle_1_deg6.883
r_scangle_it3.987
r_mcangle_it3.092
r_scbond_it2.847
r_mcbond_it2.13
r_angle_refined_deg1.767
r_nbtor_refined0.317
r_symmetry_xyhbond_nbd_refined0.291
r_nbd_refined0.214
r_xyhbond_nbd_refined0.214
r_symmetry_nbd_refined0.207
r_chiral_restr0.098
r_gen_planes_refined0.012
r_bond_refined_d0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2411
Nucleic Acid Atoms
Solvent Atoms399
Heterogen Atoms53

Software

Software
Software NamePurpose
REFMACrefinement
DIALSdata reduction
DIALSdata scaling
MOLREPphasing