7ZSJ | pdb_00007zsj

Structure of Orange Carotenoid Protein with canthaxanthin bound after 10 minutes of illumination

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4XB5

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.5	293	100 mM sodium acetate pH 4.5, 10 % poly-ethylene glycol 20,000, 3 % glycerol

Crystal Properties
Matthews coefficient	Solvent content
2.47	50.26

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 82.26	α = 90
b = 82.26	β = 90
c = 86.25	γ = 120

Symmetry
Space Group	P 32 2 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS EIGER2 XE 16M		2019-07-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.9795	Diamond	I03

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)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	1.37	29.86	100	0.046	0.048	0.015	24.6	19.2		71802

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)	Redundancy	Number Unique Reflections (All)
1	1.37	1.41			2.561	2.74	0.966

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	4XB5	1.41	28.767	65306	3207	99.884	0.193	0.1908	0.19	0.2301	0.23	31.033

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]
0.068	0.034		0.068		-0.22

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.192
r_dihedral_angle_4_deg	18.319
r_dihedral_angle_3_deg	13.493
r_lrange_it	7.545
r_dihedral_angle_1_deg	6.883
r_scangle_it	3.987
r_mcangle_it	3.092
r_scbond_it	2.847
r_mcbond_it	2.13
r_angle_refined_deg	1.767

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.192
r_dihedral_angle_4_deg	18.319
r_dihedral_angle_3_deg	13.493
r_lrange_it	7.545
r_dihedral_angle_1_deg	6.883
r_scangle_it	3.987
r_mcangle_it	3.092
r_scbond_it	2.847
r_mcbond_it	2.13
r_angle_refined_deg	1.767
r_nbtor_refined	0.317
r_symmetry_xyhbond_nbd_refined	0.291
r_nbd_refined	0.214
r_xyhbond_nbd_refined	0.214
r_symmetry_nbd_refined	0.207
r_chiral_restr	0.098
r_gen_planes_refined	0.012
r_bond_refined_d	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2411
Nucleic Acid Atoms
Solvent Atoms	399
Heterogen Atoms	53

Software

Software
Software Name	Purpose
REFMAC	refinement
DIALS	data reduction
DIALS	data scaling
MOLREP	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.