6VCH

Crystal structure of Nitrosotalea devanaterra carotenoid cleavage dioxygenase in complex with 3-hydroxy-beta-apo-14'-carotenal

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		294.15	22% Sokalan PA 25 CL 0.1 M Mes-NaOH pH 6 0.1 M NaCl 13% Xylitol 5% glycerol

Crystal Properties
Matthews coefficient	Solvent content
2.68	54.03

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 107.25	α = 90
b = 107.25	β = 90
c = 490.238	γ = 120

Symmetry
Space Group	P 61

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		2019-10-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS-II BEAMLINE 17-ID-2	0.979356	NSLS-II	17-ID-2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	2.35	50	99.9	0.13	0.999	12.83	10.6		131487			62

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.35	2.49	99.2		2.06	0.442	1.05

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	FOURIER SYNTHESIS	THROUGHOUT	6VCG	2.35	49.13	124967	6518	99.86	0.214	0.2129	0.2337	RANDOM	76.413

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]
0.22	0.11		0.22		-0.7

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.311
r_dihedral_angle_4_deg	15.103
r_dihedral_angle_3_deg	13.434
r_dihedral_angle_1_deg	8.06
r_angle_refined_deg	1.297
r_angle_other_deg	1.138
r_chiral_restr	0.048
r_bond_refined_d	0.005
r_gen_planes_refined	0.004
r_bond_other_d	0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.311
r_dihedral_angle_4_deg	15.103
r_dihedral_angle_3_deg	13.434
r_dihedral_angle_1_deg	8.06
r_angle_refined_deg	1.297
r_angle_other_deg	1.138
r_chiral_restr	0.048
r_bond_refined_d	0.005
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	21250
Nucleic Acid Atoms
Solvent Atoms	443
Heterogen Atoms	106

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
REFMAC	phasing

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.