7ZTQ

Crystal structure of the carotenoid-binding protein domain from silkworm Bombyx mori (BmCBP) in the apoform

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5I9J

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		288	5% v/v Tacsimate, pH 7.0, 0.1 M HEPES, pH 7.0, 10% w/v Polyethylene glycol monomethyl ether 5000

Crystal Properties
Matthews coefficient	Solvent content
2.36	47.99

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 65.911	α = 90
b = 67.326	β = 90
c = 121.637	γ = 90

Symmetry
Space Group	C 2 2 21

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		2021-06-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-2	0.873128	ESRF	ID23-2

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	1.45	47.1	99.7	0.039	0.043	0.017	1	20.7	6.3		47986

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	1.45	1.48	94.8		1.124	1.267	0.569	0.497		4.6

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	5I9J	1.45	47.1	45518	2428	99.66	0.1458	0.1433	0.1931	RANDOM	25.92

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]
0.79			-0.33		-0.45

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	14.706
r_dihedral_angle_2_deg	10.482
r_dihedral_angle_1_deg	7.949
r_rigid_bond_restr	5.597
r_angle_refined_deg	2.196
r_angle_other_deg	1.499
r_chiral_restr	0.127
r_gen_planes_refined	0.016
r_bond_refined_d	0.014
r_bond_other_d	0.014

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	14.706
r_dihedral_angle_2_deg	10.482
r_dihedral_angle_1_deg	7.949
r_rigid_bond_restr	5.597
r_angle_refined_deg	2.196
r_angle_other_deg	1.499
r_chiral_restr	0.127
r_gen_planes_refined	0.016
r_bond_refined_d	0.014
r_bond_other_d	0.014
r_gen_planes_other	0.011

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1862
Nucleic Acid Atoms
Solvent Atoms	215
Heterogen Atoms	6

Software

Software
Software Name	Purpose
Aimless	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
DIALS	data reduction

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.