2ZJ0 | pdb_00002zj0

Crystal structure of Mycobacterium tuberculosis S-Adenosyl-L-homocysteine hydrolase in ternary complex with NAD and 2-fluoroadenosine

X-RAY DIFFRACTION

---

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	8.5	291.5	0.2 M Magnesium chloride, 0.1 M Tris-HCl pH 8.5, 25% w/v PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 291.5K

Crystal Properties
Matthews coefficient	Solvent content
2.49	50.53

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 96.254	α = 90
b = 112.079	β = 95.15
c = 100.451	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	2.42	100	91.9	0.0809	0.0809	10.52		74187	70373		2	35.92

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	2.42	2.49	79.54		0.406	0.406

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 (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 3CE6	2.42	33.15	70373	70373	3728	91.91	0.19804	0.19373	0.19	0.27993	0.28	RANDOM	38.276

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]
2.49		0.33	-1.09		-1.34

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.614
r_dihedral_angle_4_deg	20.108
r_dihedral_angle_3_deg	17.656
r_dihedral_angle_1_deg	7.01
r_scangle_it	3.074
r_scbond_it	1.967
r_angle_refined_deg	1.699
r_mcangle_it	1.204
r_mcbond_it	0.702
r_nbtor_refined	0.306
r_symmetry_hbond_refined	0.27
r_nbd_refined	0.242
r_symmetry_vdw_refined	0.194
r_xyhbond_nbd_refined	0.168
r_chiral_restr	0.108
r_bond_refined_d	0.016
r_gen_planes_refined	0.005
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	14996
Nucleic Acid Atoms
Solvent Atoms	711
Heterogen Atoms	256

Software

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