6VCG

Crystal structure of Nitrosotalea devanaterra carotenoid cleavage dioxygenase, cobalt form

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		294	22% Sokalan PA 25 CL 0.1 M MES-NaOH pH 6 0.1 M NaCl 10% xylitol 5% glycerol

Crystal Properties
Matthews coefficient	Solvent content
2.56	51.96

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 108.01	α = 90
b = 108.01	β = 90
c = 491.61	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		2019-08-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS-II BEAMLINE 17-ID-2	0.979364	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	2.3	50	99.8	0.143	0.998	10.59	8.8		142530			61

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	2.3	2.44	98.8		2.173	0.44	0.79

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	6VCF	2.3	49.44	135427	7076	99.78	0.2384	0.2376	0.2538	RANDOM	69.28

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]
-0.65	-0.32		-0.65		2.09

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.013
r_dihedral_angle_4_deg	15.221
r_dihedral_angle_3_deg	14.039
r_dihedral_angle_1_deg	8.022
r_angle_refined_deg	1.347
r_angle_other_deg	1.153
r_chiral_restr	0.052
r_bond_refined_d	0.006
r_gen_planes_refined	0.005
r_bond_other_d	0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.013
r_dihedral_angle_4_deg	15.221
r_dihedral_angle_3_deg	14.039
r_dihedral_angle_1_deg	8.022
r_angle_refined_deg	1.347
r_angle_other_deg	1.153
r_chiral_restr	0.052
r_bond_refined_d	0.006
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	21144
Nucleic Acid Atoms
Solvent Atoms	460
Heterogen Atoms	10

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
REFMAC	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 R01GM133198.