5GG9

Crystal structure of Mycobacterium smegmatis MutT1 in complex with 8-oxo-GTP, 8-oxo-GMP and pyrophosphate

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	MICROBATCH	8.5	293	0.2 M sodium acetate trihydrate, 0.1 M TRIS hydrochloride, 30% w/v PEG 4000

Crystal Properties
Matthews coefficient	Solvent content
2.03	39.43

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 42.01	α = 90
b = 83.95	β = 92.98
c = 44	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	100	CCD	MARMOSAIC 225 mm CCD		2015-02-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE BM14	0.95372	ESRF	BM14

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.6	43.94	99.9	10.8	4.5		40162

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	1.6	1.69	100		2.1	4.5

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	3FJY	1.6	43.94	38109	2013	99.86	0.16732	0.16526	0.20596	RANDOM	28.233

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]
-1.2		0.91	-0.35		1.45

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.449
r_dihedral_angle_4_deg	16.763
r_dihedral_angle_3_deg	15.307
r_dihedral_angle_1_deg	6.595
r_long_range_B_refined	6.563
r_long_range_B_other	6.37
r_scangle_other	4.857
r_mcangle_it	3.214
r_mcangle_other	3.214
r_scbond_other	3.161
r_scbond_it	3.152
r_mcbond_it	2.222
r_mcbond_other	2.218
r_angle_refined_deg	1.977
r_angle_other_deg	0.871
r_chiral_restr	0.112
r_bond_refined_d	0.016
r_gen_planes_refined	0.009
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2305
Nucleic Acid Atoms
Solvent Atoms	338
Heterogen Atoms	68

Software

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