2ZJ1

Crystal structure of Mycobacterium tuberculosis S-adenosyl-L-homocysteine hydrolase in ternary complex with NAD and 3'-keto-aristeromycin

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3CE6	PDB entry 3CE6

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	291.5	20% PEG 1000, 200 mM Imidazole pH 8.0, 100 mM Calcium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 291.5K

Crystal Properties
Matthews coefficient	Solvent content
2.44	49.56

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 94.854	α = 90
b = 111.85	β = 96.49
c = 100.403	γ = 90

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	120	CCD	ADSC QUANTUM 315	Mirrors	2005-03-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.96400	APS	19-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2.01	100	98.86	0.0671	0.0671	10.12		136379	129513		2	25.64

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	2.01	2.06	89.41		0.353	0.353

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 3CE6	2.01	34.59	129513	129513	6853	98.86	0.19249	0.18961	0.2468	RANDOM	27.473

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]
2.17		-0.19	-1.17		-1.04

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.003
r_dihedral_angle_4_deg	19.144
r_dihedral_angle_3_deg	14.915
r_scangle_it	7.57
r_dihedral_angle_1_deg	6.542
r_scbond_it	5.854
r_mcangle_it	4.086
r_mcbond_it	3.318
r_angle_refined_deg	1.568
r_nbtor_refined	0.297
r_symmetry_vdw_refined	0.249
r_nbd_refined	0.199
r_symmetry_hbond_refined	0.188
r_xyhbond_nbd_refined	0.141
r_chiral_restr	0.102
r_bond_refined_d	0.016
r_gen_planes_refined	0.006
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_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
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	14992
Nucleic Acid Atoms
Solvent Atoms	844
Heterogen Atoms	252

Software

Software
Software Name	Purpose
REFMAC	refinement
ADSC	data collection
HKL-2000	data reduction
HKL-2000	data scaling
AMoRE	phasing