7ZSF

Structure of Orange Carotenoid Protein with canthaxanthin bound


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
2.550.89

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 82.569α = 90
b = 82.569β = 90
c = 87.365γ = 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
21x-ray50PIXELDECTRIS PILATUS 12M2020-07-29MSINGLE WAVELENGTH
31x-ray50PIXELDECTRIS PILATUS 12M2020-07-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.9796DiamondI03
2SYNCHROTRONDIAMOND BEAMLINE I234.42801DiamondI23
3SYNCHROTRONDIAMOND BEAMLINE I234.27532DiamondI23

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
11.3687.2999.970.0750.0790.02517.119.974252
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.361.41003.5433.480.7790.5191.119.9

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-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT4XB51.3655.39674207369999.8840.190.1890.2179RANDOM25.954
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]
0.0010.001-0.003
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.514
r_dihedral_angle_4_deg16.814
r_dihedral_angle_3_deg12.579
r_lrange_it7.807
r_dihedral_angle_1_deg5.822
r_scangle_it4.593
r_scbond_it3.173
r_mcangle_it3.096
r_mcbond_it2.152
r_angle_refined_deg1.957
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.514
r_dihedral_angle_4_deg16.814
r_dihedral_angle_3_deg12.579
r_lrange_it7.807
r_dihedral_angle_1_deg5.822
r_scangle_it4.593
r_scbond_it3.173
r_mcangle_it3.096
r_mcbond_it2.152
r_angle_refined_deg1.957
r_nbtor_refined0.314
r_symmetry_nbd_refined0.275
r_nbd_refined0.215
r_xyhbond_nbd_refined0.208
r_symmetry_xyhbond_nbd_refined0.205
r_chiral_restr0.117
r_bond_refined_d0.012
r_gen_planes_refined0.011
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2376
Nucleic Acid Atoms
Solvent Atoms388
Heterogen Atoms53

Software

Software
Software NamePurpose
REFMACrefinement
DIALSdata reduction
DIALSdata scaling
MOLREPphasing
SHELXCDphasing