5TOV | pdb_00005tov

Crystal structure of the inactive form of S-adenosyl-L-homocysteine hydrolase from Thermotoga maritima in binary complex with NADH

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1LI4

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.3	292	0.2 M MgCl2, 0.1 M sodium acetate pH 5.3 and 30% (v/v) MPD

Crystal Properties
Matthews coefficient	Solvent content
2.9	57.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 120.4	α = 90
b = 106.7	β = 109.2
c = 85.9	γ = 90

Symmetry
Space Group	C 1 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	MARMOSAIC 225 mm CCD		2010-11-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-BM	0.97242	APS	22-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	1.9	30	99.6	0.056	23.4	3.8		80548		-3	26.9

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.9	1.93

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	1LI4	1.9	30	79463	1069	99.86	0.16154	0.16108	0.17	0.19594	0.21	RANDOM	40.261

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]
1.35		-0.81	0.53		-1.06

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.661
r_dihedral_angle_4_deg	16.487
r_dihedral_angle_3_deg	13.818
r_long_range_B_refined	7.233
r_long_range_B_other	7.103
r_dihedral_angle_1_deg	6.235
r_scangle_other	4.228
r_mcangle_it	2.874
r_mcangle_other	2.873
r_scbond_it	2.691
r_scbond_other	2.691
r_mcbond_it	1.946
r_mcbond_other	1.945
r_angle_refined_deg	1.583
r_angle_other_deg	0.988
r_chiral_restr	0.098
r_bond_refined_d	0.014
r_gen_planes_refined	0.007
r_bond_other_d	0.002
r_gen_planes_other	0.002
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5877
Nucleic Acid Atoms
Solvent Atoms	491
Heterogen Atoms	46

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing