6SGM | pdb_00006sgm

Crystal structure of monooxygenase RutA complexed with 4-Thiouracil.

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		295	100 mM Bis-Tris pH 6.5, 1900 mM ammonium sulphate, 2-5% MPD (v/v),1 mM FMN, 1 mM 4-Thiouracil

Crystal Properties
Matthews coefficient	Solvent content
2.66	53.72

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 87.567	α = 90
b = 87.567	β = 90
c = 95.999	γ = 120

Symmetry
Space Group	P 31 2 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		2018-11-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06SA	1.0	SLS	X06SA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	48	100	0.99	22.1	19.8		29258

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2	2.11			0.953

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	5WAN	2	43.822	29228	1386	99.99	0.205	0.2027	0.2	0.2454	0.25	42.855

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]
0.144	0.072		0.144		-0.466

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.215
r_dihedral_angle_4_deg	19.4
r_dihedral_angle_3_deg	13.928
r_dihedral_angle_1_deg	6.739
r_angle_refined_deg	1.698
r_nbtor_refined	0.317
r_nbd_refined	0.214
r_symmetry_nbd_refined	0.196
r_chiral_restr	0.126
r_xyhbond_nbd_refined	0.121

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.215
r_dihedral_angle_4_deg	19.4
r_dihedral_angle_3_deg	13.928
r_dihedral_angle_1_deg	6.739
r_angle_refined_deg	1.698
r_nbtor_refined	0.317
r_nbd_refined	0.214
r_symmetry_nbd_refined	0.196
r_chiral_restr	0.126
r_xyhbond_nbd_refined	0.121
r_symmetry_xyhbond_nbd_refined	0.076
r_bond_refined_d	0.01
r_gen_planes_refined	0.01

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2587
Nucleic Acid Atoms
Solvent Atoms	99
Heterogen Atoms	39

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
PHASER	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.