Experiment: 4YWN

Crystal structure of NADH-FMN oxidoreductase from Mycobacterium avium

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3PFT	PDB entry 3PFT

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.4	290	20 mg/mL MyavA.00250.a.A1.PS00591 against JCSG a3 (optimization: 22% PEG3350, 200 mM ammonium citrate dibasic), cryoprotectant: 20% ethylene glycol, tray 247348, puck wuf3-10

Crystal Properties
Matthews coefficient	Solvent content
2.08	41

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 50.26	α = 90
b = 50.26	β = 90
c = 229.59	γ = 90

Symmetry
Space Group	P 41 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	RAYONIX MX-225		2015-02-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-G	0.978720	APS	21-ID-G

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	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	1.8	50	99.9	0.072	0.075	20.56	11.7	28629	28598		-3	24.69

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.8	1.85	99.9		0.472	0.493	4.93	12

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	PDB entry 3PFT	1.8	37.812	1.37	28445	1427	99.75	0.1806	0.1788	0.1817	0.2153	0.2179	Random selection	36.0889

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	11.695
f_angle_d	0.993
f_chiral_restr	0.049
f_bond_d	0.006
f_plane_restr	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2016
Nucleic Acid Atoms
Solvent Atoms	125
Heterogen Atoms	13

Software

Software
Software Name	Purpose
XDS	data scaling
XSCALE	data scaling
PHASER	phasing
ARP	model building
Coot	model building
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction