3CI4 | pdb_00003ci4

Structure of the PduO-type ATP:co(I)rrinoid adenosyltransferase from Lactobacillus reuteri complexed with four-coordinate cob(II)inamide and ATP

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	6	300	ANOXIC, 13% PEG 8000, 0.1 M MES, 200 mM KCl, 33 ug/mL FMN reductase, 20 mM NADH, 2 mM FMN, 2 mM dicyanocobinamide, 2 mM MgCl2, 2 mM ATP, pH 6, VAPOR DIFFUSION, temperature 300K

Crystal Properties
Matthews coefficient	Solvent content
2.2	44.1

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 67.826	α = 90
b = 67.826	β = 90
c = 111.26	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	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 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	2	30	98.2	0.109	5.7	2.5		13603

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)
	2		99.9		0.26	1.7	1.5

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	2	30	12024	622	98.22	0.17188	0.16996	0.17	0.20927	0.21	RANDOM	8.122

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]
0.21			0.21		-0.32

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.657
r_dihedral_angle_4_deg	17.22
r_dihedral_angle_3_deg	12.043
r_dihedral_angle_1_deg	10.019
r_scangle_it	2.523
r_angle_refined_deg	1.993
r_scbond_it	1.724
r_mcangle_it	0.993
r_mcbond_it	0.57
r_nbtor_refined	0.304
r_symmetry_vdw_refined	0.233
r_nbd_refined	0.216
r_chiral_restr	0.197
r_symmetry_hbond_refined	0.131
r_xyhbond_nbd_refined	0.116
r_symmetry_metal_ion_refined	0.094
r_metal_ion_refined	0.078
r_bond_refined_d	0.013
r_gen_planes_refined	0.007
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1481
Nucleic Acid Atoms
Solvent Atoms	85
Heterogen Atoms	101

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
PROTEUM PLUS	data collection
PROTEUM PLUS	data reduction
PROTEUM PLUS	data scaling
MOLREP	phasing