6TIL

Structure of A. niger Fdc WT in complex with FMN and 2 naphthoic acid

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4ZAA

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	0.2 M potassium thiocyanate, Bis-Tris propane pH 6.5, 20% w/v PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.34	47.46

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 95.628	α = 90
b = 63.183	β = 90
c = 87.318	γ = 90

Symmetry
Space Group	P 21 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	PIXEL	DECTRIS PILATUS 6M-F		2018-04-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.90	Diamond	I03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Rrim 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	1.42	64.55	99.3	0.123	1	6.4	4.4		99700

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.42	1.44	97.6		0.792	0.6	1.6	4.4

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	FOURIER SYNTHESIS	FREE R-VALUE	4ZAA	1.42	64.481	99668	4919	99.301	0.154	0.1517	0.1997	16.807

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]
0.286			-0.46		0.174

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.728
r_dihedral_angle_4_deg	21.4
r_dihedral_angle_3_deg	12.256
r_dihedral_angle_1_deg	6.824
r_rigid_bond_restr	4.487
r_lrange_it	4.452
r_lrange_other	4.451
r_scangle_other	3.637
r_scangle_it	3.634
r_scbond_it	3.206
r_scbond_other	3.206
r_mcangle_other	2.849
r_mcangle_it	2.846
r_mcbond_it	2.471
r_mcbond_other	2.46
r_angle_refined_deg	2.006
r_angle_other_deg	1.614
r_symmetry_nbd_refined	0.26
r_nbd_refined	0.244
r_nbd_other	0.24
r_symmetry_xyhbond_nbd_refined	0.227
r_xyhbond_nbd_refined	0.209
r_symmetry_nbd_other	0.198
r_nbtor_refined	0.176
r_chiral_restr	0.119
r_metal_ion_refined	0.093
r_symmetry_nbtor_other	0.085
r_symmetry_metal_ion_refined	0.053
r_bond_refined_d	0.019
r_gen_planes_refined	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	3804
Nucleic Acid Atoms
Solvent Atoms	464
Heterogen Atoms	47

Software

Software
Software Name	Purpose
REFMAC	refinement
DIALS	data reduction
DIALS	data scaling