6TIO | pdb_00006tio

Structure of A. niger Fdc Wt in complex with FMN and benzothiophene 2 carboxylic 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	47.53

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 95.39	α = 90
b = 63.283	β = 90
c = 87.501	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	0.9	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	1.54	95.57	99.8	0.136	1	6.9	5		78889

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	1.54	1.57			0.816	0.5	1.7

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	FREE R-VALUE	4ZAA	1.54	64.482	78838	3869	99.736	0.15	0.1479	0.16	0.1951	0.2	18.2

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]
0.328			-0.449		0.121

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.54
r_dihedral_angle_4_deg	22.344
r_dihedral_angle_3_deg	12.437
r_dihedral_angle_1_deg	6.788
r_lrange_it	4.663
r_lrange_other	4.662
r_rigid_bond_restr	3.838
r_scangle_it	3.745
r_scangle_other	3.742
r_mcangle_other	3.405
r_mcangle_it	3.404
r_scbond_it	3.291
r_scbond_other	3.291
r_mcbond_it	2.841
r_mcbond_other	2.835
r_angle_refined_deg	1.98
r_angle_other_deg	1.59
r_symmetry_nbd_refined	0.245
r_nbd_refined	0.239
r_symmetry_xyhbond_nbd_refined	0.238
r_nbd_other	0.222
r_xyhbond_nbd_refined	0.197
r_symmetry_nbd_other	0.194
r_nbtor_refined	0.171
r_chiral_restr	0.113
r_metal_ion_refined	0.102
r_symmetry_nbtor_other	0.085
r_symmetry_metal_ion_refined	0.076
r_symmetry_xyhbond_nbd_other	0.038
r_bond_refined_d	0.016
r_gen_planes_refined	0.014
r_gen_planes_other	0.003
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3807
Nucleic Acid Atoms
Solvent Atoms	463
Heterogen Atoms	46

Software

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