8CQS

Flavin mononucleotide-dependent nitroreductase B.thetaiotaomicron (BT_0217)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	5.5	293	12mM sodium nitrate, 12mM sodium phosphate, 12mM ammonium sulphate

Crystal Properties
Matthews coefficient	Solvent content
1.97	37.54

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 80.03	α = 90
b = 44.41	β = 110.739
c = 103.04	γ = 90

Symmetry
Space Group	C 1 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		2021-04-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1)	0.976200	PETRA III, EMBL c/o DESY	P13 (MX1)

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	1.7	38.193	99.1	0.184	0.202	0.081	0.994	9.7	10.4		37180

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	1.7	1.73			0.534	0.716	0.471	0.813		2.8

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	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	AF-Q8AB93-F1	1.7	38.193	37180	1777	99.07	0.151	0.1492	0.182	22.224

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]
-0.871		0.225	-0.131		0.646

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	15.536
r_dihedral_angle_6_deg	15.365
r_dihedral_angle_2_deg	7.965
r_lrange_it	6.284
r_dihedral_angle_1_deg	6.28
r_lrange_other	6.266
r_scangle_it	5.633
r_scangle_other	5.549
r_scbond_it	3.766
r_scbond_other	3.708
r_mcangle_it	2.809
r_mcangle_other	2.809
r_mcbond_it	2.076
r_mcbond_other	2.076
r_angle_refined_deg	1.91
r_angle_other_deg	0.658
r_symmetry_xyhbond_nbd_refined	0.271
r_symmetry_nbd_refined	0.233
r_nbd_refined	0.227
r_nbd_other	0.19
r_nbtor_refined	0.18
r_symmetry_nbd_other	0.177
r_symmetry_xyhbond_nbd_other	0.175
r_xyhbond_nbd_refined	0.123
r_chiral_restr	0.105
r_ncsr_local_group_1	0.102
r_symmetry_nbtor_other	0.08
r_gen_planes_refined	0.017
r_bond_refined_d	0.014
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2913
Nucleic Acid Atoms
Solvent Atoms	162
Heterogen Atoms	72

Software

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