2R6T | pdb_00002r6t

Structure of a R132K 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	46.17

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 64.678	α = 90
b = 64.678	β = 90
c = 169.197	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	8.3	18.5	6.3		12134			30.3

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	2.68	97.4		22.9	6.5	4.6

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	MOLECULAR REPLACEMENT	THROUGHOUT	2.61	30	11416	540	94.18	0.192	0.189	0.19	0.259	0.26	RANDOM	22.579

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]
0.1	0.05		0.1		-0.15

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.127
r_dihedral_angle_3_deg	15.597
r_dihedral_angle_4_deg	11.06
r_dihedral_angle_1_deg	5.767
r_scangle_it	1.966
r_angle_refined_deg	1.43
r_scbond_it	1.299
r_mcangle_it	0.853
r_mcbond_it	0.481
r_nbtor_refined	0.301

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.127
r_dihedral_angle_3_deg	15.597
r_dihedral_angle_4_deg	11.06
r_dihedral_angle_1_deg	5.767
r_scangle_it	1.966
r_angle_refined_deg	1.43
r_scbond_it	1.299
r_mcangle_it	0.853
r_mcbond_it	0.481
r_nbtor_refined	0.301
r_nbd_refined	0.208
r_symmetry_vdw_refined	0.189
r_symmetry_hbond_refined	0.179
r_xyhbond_nbd_refined	0.152
r_chiral_restr	0.085
r_metal_ion_refined	0.044
r_bond_refined_d	0.012
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2735
Nucleic Acid Atoms
Solvent Atoms	115
Heterogen Atoms	66

Software

Software
Software Name	Purpose
SAINT	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

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.