7P9Q | pdb_00007p9q

Crystal structure of Indole 3-Carboxylic acid decarboxylase from Arthrobacter nicotianae FI1612 in complex with co-factor prFMN.

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7ABO

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	293	0.1 Carboxylic acid, 0.1 M Buffer System pH 6.5, 30% Precipitant mixture 3

Crystal Properties
Matthews coefficient	Solvent content
3.17	61.23

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 104.2	α = 90
b = 195.45	β = 116.35
c = 105.21	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	80	PIXEL	DECTRIS EIGER2 XE 16M		2017-07-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.9762	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	2.53	43.42	98.86	0.994	8.6	3.4		123931

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	2.53	2.57			0.39

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	MOLECULAR REPLACEMENT	THROUGHOUT	7ABO	2.53	43.42	117399	6529	98.79	0.1858	0.1839	0.19	0.221	0.22	RANDOM	84.096

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]
0.03		-1.32	3.27		-1.34

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.026
r_dihedral_angle_4_deg	17.79
r_dihedral_angle_3_deg	17.063
r_dihedral_angle_1_deg	7.23
r_angle_refined_deg	1.701
r_angle_other_deg	1.365
r_chiral_restr	0.074
r_bond_refined_d	0.011
r_gen_planes_refined	0.008
r_bond_other_d	0.002

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.026
r_dihedral_angle_4_deg	17.79
r_dihedral_angle_3_deg	17.063
r_dihedral_angle_1_deg	7.23
r_angle_refined_deg	1.701
r_angle_other_deg	1.365
r_chiral_restr	0.074
r_bond_refined_d	0.011
r_gen_planes_refined	0.008
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	20763
Nucleic Acid Atoms
Solvent Atoms	477
Heterogen Atoms	228

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.