8CQV

Flavin mononucleotide-dependent nitroreductase B.thetaiotaomicron (BT_3392)

X-RAY DIFFRACTION

---

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	6.5	293	Buffer system (Imidazol, MES) 20% v/v Ethylen glycol, 10% v/v PEG 8000, 0.12M Diethylene glycol, 0.12M Triethylene glycol, 0.12M Tetraethylene glycol, 0.12M Pentaethylene glycol

Crystal Properties
Matthews coefficient	Solvent content
2.12	41.94

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 64.894	α = 90
b = 40.623	β = 99.996
c = 75.497	γ = 90

Symmetry
Space Group	P 1 21 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		2021-06-08	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	74.35	100	0.106	0.132	0.078	0.996	8.8	5		43098

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			1.556	1.966	1.186	0.342		4.7

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-Q8A2B3-F1	1.7	53.306	43072	2125	99.942	0.173	0.1719	0.2063	23.021

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]
-0.78		-0.414	0.934		-0.007

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.33
r_dihedral_angle_3_deg	14.757
r_dihedral_angle_2_deg	12.083
r_dihedral_angle_1_deg	6.388
r_lrange_it	6.288
r_lrange_other	6.288
r_scangle_it	5.006
r_scangle_other	5.005
r_scbond_it	3.419
r_scbond_other	3.418
r_mcangle_other	2.445
r_mcangle_it	2.442
r_mcbond_it	1.798
r_mcbond_other	1.795
r_angle_refined_deg	1.793
r_angle_other_deg	0.695
r_symmetry_xyhbond_nbd_refined	0.23
r_symmetry_nbd_refined	0.225
r_nbd_refined	0.224
r_metal_ion_refined	0.194
r_nbd_other	0.193
r_nbtor_refined	0.183
r_xyhbond_nbd_refined	0.175
r_symmetry_nbd_other	0.166
r_chiral_restr	0.102
r_ncsr_local_group_1	0.094
r_symmetry_nbtor_other	0.075
r_symmetry_metal_ion_refined	0.061
r_gen_planes_refined	0.02
r_bond_refined_d	0.014
r_bond_other_d	0.003
r_gen_planes_other	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3247
Nucleic Acid Atoms
Solvent Atoms	145
Heterogen Atoms	150

Software

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