6R3N | pdb_00006r3n

Aspergillus niger ferulic acid decarboxylase (Fdc) in complex with the covalent adduct formed between prFMN cofactor and butynoic acid (Int1')

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4ZA9

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		277	0.2 M POTASSIUM THIOCYANATE, BIS-TRIS PROPANE 6.5, 20 % W/V PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.38	48.41

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 95.874	α = 90
b = 63.892	β = 90
c = 87.714	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 300K		2018-07-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.9795	Diamond	I04

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	1.02	43.86	87.03	0.995	9.3	4.8		237279

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.02	1.056	14.7		0.647	1.4	2.4

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	THROUGHOUT	4ZA9	1.02	43.86	225462	11889	86.04	0.1355	0.13489	0.14	0.1471	0.15	RANDOM	11.971

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]
-0.22			-0.07		0.29

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_free	42.382
r_dihedral_angle_2_deg	33.27
r_dihedral_angle_4_deg	22.095
r_rigid_bond_restr	15.27
r_dihedral_angle_3_deg	12.109
r_sphericity_bonded	9.278
r_dihedral_angle_1_deg	6.5
r_angle_refined_deg	2.084
r_angle_other_deg	0.992
r_chiral_restr	0.305
r_bond_refined_d	0.021
r_gen_planes_refined	0.013
r_gen_planes_other	0.004
r_bond_other_d	0.003
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_it
r_mcbond_other
r_mcangle_it
r_mcangle_other
r_scbond_it
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3844
Nucleic Acid Atoms
Solvent Atoms	478
Heterogen Atoms	82

Software

Software
Software Name	Purpose
REFMAC	refinement
xia2	data reduction
xia2	data scaling