6V43

Crystal structure of the flavin oxygenase with cofactor and substrate bound involved in folate catabolism

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6V42

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	298	0.1M TRIS hydrochloride pH 8.5, 2.0M ammonium sulfate

Crystal Properties
Matthews coefficient	Solvent content
2.37	48.12

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 61.56	α = 90
b = 125.38	β = 90
c = 127.31	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	120	IMAGE PLATE	RIGAKU RAXIS IV++		2018-11-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007	1.542

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	1.77	61.56	94.8	0.19	0.206	0.079	0.971	6.1	6.4		90846			18.66

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	1.77	1.8	78.2		0.993	1.106	0.473	0.605		5

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	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	6V42	1.77	34.94	1.34	90413	4570	94.13	0.1628	0.1608	0.2023	25.17

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	16.0812
f_angle_d	0.9505
f_chiral_restr	0.0582
f_bond_d	0.0079
f_plane_restr	0.0058

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7276
Nucleic Acid Atoms
Solvent Atoms	1131
Heterogen Atoms	130

Software

Software
Software Name	Purpose
PHENIX	refinement
MOSFLM	data reduction
Aimless	data scaling
PDB_EXTRACT	data extraction
PHENIX	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.