2R6X

Structure of a D35N variant PduO-type ATP:co(I)rrinoid adenosyltransferase from Lactobacillus reuteri complexed with ATP

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	6	300	ANOXIC, 16% PEG 8000, 0.1 M MES, 200 mM KCl, 30 ug/mL FMN reductase, 50 mM NADH, 10 mM FMN, 10 mM hydroxycobalamin, 10 mM MgCl2, 10 mM ATP, pH 6.0, vapor diffusion, temperature 300K

Crystal Properties
Matthews coefficient	Solvent content
2.29	46.34

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 64.772	α = 90
b = 64.772	β = 90
c = 169.438	γ = 120

Symmetry
Space Group	P 63

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	Bruker Platinum 135	Montel	2007-05-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU200

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym I (Observed)	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	2.61	30	99.6	6.8	26.1	7.5		12422			29.4

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.61	2.66	99.5		0.177		4.9

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION		THROUGHOUT	2.61	30	11938	579	96.18	0.177	0.173	0.249	RANDOM	30.817

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]
0.54	0.27		0.54		-0.81

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.574
r_dihedral_angle_4_deg	19.178
r_dihedral_angle_3_deg	15.679
r_dihedral_angle_1_deg	5.703
r_scangle_it	2.114
r_scbond_it	1.499
r_angle_refined_deg	1.395
r_mcangle_it	0.859
r_mcbond_it	0.593
r_nbtor_refined	0.303

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.574
r_dihedral_angle_4_deg	19.178
r_dihedral_angle_3_deg	15.679
r_dihedral_angle_1_deg	5.703
r_scangle_it	2.114
r_scbond_it	1.499
r_angle_refined_deg	1.395
r_mcangle_it	0.859
r_mcbond_it	0.593
r_nbtor_refined	0.303
r_nbd_refined	0.201
r_symmetry_vdw_refined	0.197
r_symmetry_hbond_refined	0.192
r_xyhbond_nbd_refined	0.183
r_chiral_restr	0.094
r_symmetry_metal_ion_refined	0.091
r_bond_refined_d	0.012
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2781
Nucleic Acid Atoms
Solvent Atoms	139
Heterogen Atoms	66

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.