6DYY | pdb_00006dyy

Crystal structure of Helicobacter pylori 5'-methylthioadenosine/S-adenosyl homocysteine nucleosidase (MTAN) complexed with (3R,4S)-1-((4-amino-5H-pyrrolo[3,2-d]pyrimidin-7-yl)methyl)-4-(((3-(1-butyl-1H-1,2,3-triazol-4-yl)propyl)thio)methyl)pyrrolidin-3-ol

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4WKP	PDB entry 4WKP

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		295	200 mM calcium chloride, 20% w/v PEG3350

Crystal Properties
Matthews coefficient	Solvent content
2.2	44.31

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 72.564	α = 90
b = 74.028	β = 90
c = 176.887	γ = 90

Symmetry
Space Group	P 21 21 21

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	RAYONIX MX225HE	KB mirrors	2017-10-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 31-ID	0.97931	APS	31-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	CC (Half)	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	1.61	88.44	100	0.99	11.4	7.4		123910

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.61	1.64			0.8	2.1

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	PDB entry 4WKP	1.61	88.44	117541	6265	99.95	0.18048	0.17927	0.19	0.20328	0.21	RANDOM	23.601

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]
-0.41			1.88		-1.47

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.434
r_dihedral_angle_4_deg	16.417
r_dihedral_angle_3_deg	12.969
r_dihedral_angle_1_deg	5.731
r_long_range_B_refined	4.887
r_long_range_B_other	4.887
r_scangle_other	3.261
r_scbond_it	2.053
r_scbond_other	2.053
r_mcangle_it	2
r_mcangle_other	2
r_angle_refined_deg	1.49
r_mcbond_it	1.303
r_mcbond_other	1.303
r_angle_other_deg	0.935
r_chiral_restr	0.085
r_bond_refined_d	0.009
r_gen_planes_refined	0.005
r_bond_other_d	0.002
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7042
Nucleic Acid Atoms
Solvent Atoms	894
Heterogen Atoms	154

Software

Software
Software Name	Purpose
REFMAC	refinement
iMOSFLM	data reduction
Aimless	data scaling
PHASER	phasing