Experiment: 7QD2

Structure of the orange carotenoid protein from Planktothrix agardhii binding canthaxanthin in the P21 space group

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3MG1

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5	293	0.1 M sodium acetate, pH 5 and 10-20% PEG4000

Crystal Properties
Matthews coefficient	Solvent content
2.32	46.98

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 63.46	α = 90
b = 65.94	β = 102.262
c = 77.28	γ = 90

Symmetry
Space Group	P 1 21 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 EIGER X 16M		2019-08-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	0.9998	SLS	X10SA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	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	1.4	43.6	93.9	0.036	0.046	0.028	0.998	11.47	2.4		115206			21.13

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)	Redundancy	Number Unique Reflections (All)
1	1.4	1.45	92.54		0.3938	0.5066	0.3153	0.852	1.9	2.4

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	3mg1	1.4	43.6	1.36	115047	5753	93.9	0.2019	0.2005	0.2004	0.2302	0.2302	30.31

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]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	16.9443
f_angle_d	0.9485
f_chiral_restr	0.0788
f_plane_restr	0.0091
f_bond_d	0.0069

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4781
Nucleic Acid Atoms
Solvent Atoms	596
Heterogen Atoms	100

Software

Software
Software Name	Purpose
PHENIX	refinement
PHASER	phasing
XSCALE	data scaling
XDS	data reduction