3GAI | pdb_00003gai

Structure of a F112A variant PduO-type ATP:corrinoid adenosyltransferase from Lactobacillus reuteri complexed with cobalamin and ATP

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6	298	anoxic, 14% PEG 8000, 0.2M potassium chloride, 0.1 M MES, 30 ug/mL E. coli FMN reductase, 50 mM NADH, 10 mM FMN, 10 mM hydoxycobalamin, 10 mM ATP, 10 mM magnesium chloride, 0.3 M sodium chloride , pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.52	51.24

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 80.745	α = 90
b = 80.745	β = 90
c = 89.693	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	298	CCD	SBC-3		2007-08-17	M	SINGLE WAVELENGTH

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

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	1.48	50	99.7	0.057	46.235	5.6		36190

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	1.48	1.53	98.6		0.128		5	3618

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	1.48	30	36185	1804	99.69	0.157	0.156	0.16	0.174	0.17	RANDOM	19.396

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]
0.4	0.2		0.4		-0.6

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.177
r_dihedral_angle_4_deg	16.272
r_dihedral_angle_3_deg	11.802
r_dihedral_angle_1_deg	4.955
r_scangle_it	3.477
r_scbond_it	2.342
r_angle_refined_deg	2.201
r_mcangle_it	1.471
r_mcbond_it	0.828
r_nbtor_refined	0.316
r_chiral_restr	0.271
r_nbd_refined	0.236
r_symmetry_vdw_refined	0.235
r_xyhbond_nbd_refined	0.192
r_symmetry_metal_ion_refined	0.178
r_symmetry_hbond_refined	0.136
r_metal_ion_refined	0.134
r_bond_refined_d	0.014
r_gen_planes_refined	0.01

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1463
Nucleic Acid Atoms
Solvent Atoms	159
Heterogen Atoms	145

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction