7ZSG

Structure of Orange Carotenoid Protein with canthaxanthin bound after 1 minute 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
2.5251.17

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 82.58α = 90
b = 82.58β = 90
c = 87.22γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 XE 16M2019-06-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.979DiamondI04

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
11.3271.491000.0490.0510.01623.818.780954
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)
11.321.391002.4482.6611.021.212.9

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-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT4XB51.3955.36469455344599.9270.1940.1940.19728.063
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]
0.0120.0060.012-0.038
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.158
r_dihedral_angle_4_deg20.059
r_dihedral_angle_3_deg14.082
r_lrange_it7.346
r_dihedral_angle_1_deg6.839
r_scangle_it4.005
r_mcangle_it3.071
r_scbond_it2.692
r_angle_refined_deg2.325
r_mcbond_it2.012
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.158
r_dihedral_angle_4_deg20.059
r_dihedral_angle_3_deg14.082
r_lrange_it7.346
r_dihedral_angle_1_deg6.839
r_scangle_it4.005
r_mcangle_it3.071
r_scbond_it2.692
r_angle_refined_deg2.325
r_mcbond_it2.012
r_symmetry_xyhbond_nbd_refined0.357
r_nbtor_refined0.314
r_xyhbond_nbd_refined0.276
r_symmetry_nbd_refined0.254
r_nbd_refined0.216
r_chiral_restr0.149
r_bond_refined_d0.025
r_gen_planes_refined0.014
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