2NT8 | pdb_00002nt8

ATP bound at the active site of a PduO type ATP:co(I)rrinoid adenosyltransferase from Lactobacillus reuteri

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1NOG	PDB ENTRY 1NOG

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	BATCH	8.5	293	0.85 M Ammonium sulfate, 50 mM magnesium chloride, 150 mM sodium chloride, 1.5 mM ATP, 4 mM hydroxocobalamin, pH 8.5, BATCH, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.2	44.06

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 110.609	α = 90
b = 110.609	β = 90
c = 110.609	γ = 90

Symmetry
Space Group	I 2 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	SBC-3		2005-11-21	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	1.68	50	99.4	0.046	11.3	9.5		25595

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.68	1.74	99.4		0.234	0.234	4.1	6.8	2522

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	PDB ENTRY 1NOG	1.68	30	25595	1305	99.46	0.175	0.173	0.17	0.204	0.2	RANDOM	23.946

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.427
r_dihedral_angle_4_deg	14.683
r_dihedral_angle_3_deg	12.146
r_dihedral_angle_1_deg	5.209
r_scangle_it	3.699
r_scbond_it	2.654
r_mcangle_it	1.687
r_angle_refined_deg	1.341
r_mcbond_it	1.056
r_nbtor_refined	0.304

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.427
r_dihedral_angle_4_deg	14.683
r_dihedral_angle_3_deg	12.146
r_dihedral_angle_1_deg	5.209
r_scangle_it	3.699
r_scbond_it	2.654
r_mcangle_it	1.687
r_angle_refined_deg	1.341
r_mcbond_it	1.056
r_nbtor_refined	0.304
r_nbd_refined	0.208
r_symmetry_vdw_refined	0.198
r_xyhbond_nbd_refined	0.138
r_symmetry_hbond_refined	0.134
r_chiral_restr	0.084
r_bond_refined_d	0.011
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1440
Nucleic Acid Atoms
Solvent Atoms	141
Heterogen Atoms	49

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling

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.