3CI3 | pdb_00003ci3

Structure of the PduO-type ATP:co(I)rrinoid adenosyltransferase from Lactobacillus reuteri complexed with partial adenosylcobalamin and PPPi

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	6	300	ANOXIC, 10% PEG 8000, 0.1 M MES, 33 ug/mL FMN reductase, 20 mM NADH, 2 mM FMN, 2 mM hydroxycobalamin, 3 mM MgCl2, 3 mM ATP. Grown 65 days, VAPOR DIFFUSION, temperature 300K

Crystal Properties
Matthews coefficient	Solvent content
2.2	44.17

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 67.965	α = 90
b = 67.965	β = 90
c = 110.941	γ = 120

Symmetry
Space Group	H 3

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	ADSC QUANTUM 315		2006-12-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	1.541	APS	19-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	1.11	30	98.9	0.39	35.3	4.9		74669			13.9

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.11	1.15	89		0.96	9.8	2.3

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION		THROUGHOUT	1.11	30	74656	3762	99.92	0.161	0.16	0.16	0.18	0.18	RANDOM	12.935

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]
0.2	0.1		0.2		-0.3

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.127
r_dihedral_angle_4_deg	16.524
r_dihedral_angle_1_deg	12.13
r_dihedral_angle_3_deg	11.705
r_scangle_it	2.716
r_angle_refined_deg	2.429
r_scbond_it	2.159
r_mcangle_it	1.575
r_mcbond_it	1.083
r_chiral_restr	0.33

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.127
r_dihedral_angle_4_deg	16.524
r_dihedral_angle_1_deg	12.13
r_dihedral_angle_3_deg	11.705
r_scangle_it	2.716
r_angle_refined_deg	2.429
r_scbond_it	2.159
r_mcangle_it	1.575
r_mcbond_it	1.083
r_chiral_restr	0.33
r_nbtor_refined	0.318
r_nbd_refined	0.254
r_symmetry_vdw_refined	0.199
r_xyhbond_nbd_refined	0.19
r_symmetry_hbond_refined	0.156
r_bond_refined_d	0.021
r_gen_planes_refined	0.015

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1488
Nucleic Acid Atoms
Solvent Atoms	172
Heterogen Atoms	105

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

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.