3L0Z

Crystal structure of a putative Nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase from Methanocaldococcus jannaschii DSM 2661

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.5	289	0.1 M Acetate, 0.8 M NaH2PO4/1.2 K2HPO4, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
3.06	59.74

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 119.305	α = 90
b = 119.305	β = 90
c = 170.105	γ = 120

Symmetry
Space Group	P 31 2 1

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 315r	mirrors	2009-10-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.9794	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	2.65	40	99.8	0.078	35	7.1	41130	41047	2	2	75

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	2.65	2.7	100		0.7	3	7.3	2003

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	Cut-off Sigma (F)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	2.65	40	2	2	40990	38929	2061	99.36	0.205	0.20515	0.20219	0.26175	RANDOM	30.138

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]
2.66	1.33		2.66		-4

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.744
r_dihedral_angle_3_deg	19.799
r_dihedral_angle_4_deg	19.221
r_dihedral_angle_1_deg	6.749
r_scangle_it	3.337
r_scbond_it	2.021
r_angle_refined_deg	1.645
r_mcangle_it	1.361
r_angle_other_deg	0.973
r_mcbond_it	0.724
r_mcbond_other	0.127
r_chiral_restr	0.089
r_bond_refined_d	0.017
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7612
Nucleic Acid Atoms
Solvent Atoms	9
Heterogen Atoms	35

Software

Software
Software Name	Purpose
SBC-Collect	data collection
HKL-3000	phasing
DM	model building
SHELX	model building
MLPHARE	phasing
Coot	model building
RESOLVE	model building
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
DM	phasing
SHELX	phasing
RESOLVE	phasing