6M6Y | pdb_00006m6y

Crystal structure of Mycobacterium smegmatis MutT1 in complex with 8-oxo-dGTP

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5GG5

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	MICROBATCH	4.6	298	0.2 M ammonium acetate, 0.1 M sodium acetate trihydrate, 30% w/v PEG 4000

Crystal Properties
Matthews coefficient	Solvent content
2.15	41.33

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 191.909	α = 90
b = 37.1	β = 90
c = 44.73	γ = 90

Symmetry
Space Group	P 21 21 2

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		2015-05-21	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)	R Sym I (Observed)	Rrim I (All)	Rpim I (All)	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	1.5	44.73	99.9	0.101	0.11	0.042	0.995	9.9	6.7		52399

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Rrim I (All)	Rpim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.5	1.58	100		0.759	0.759	0.824	0.317	1	6.6

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	5GG5	1.5	36.45	49101	2627	98.72	0.2001	0.199	0.2003	0.2213	0.2233	RANDOM	20.638

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]
-0.94			0.37		0.56

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	27.687
r_dihedral_angle_4_deg	18.633
r_dihedral_angle_3_deg	13.977
r_dihedral_angle_1_deg	6.39
r_angle_other_deg	2.338
r_angle_refined_deg	1.879
r_chiral_restr	0.105
r_bond_other_d	0.034
r_bond_refined_d	0.016
r_gen_planes_other	0.015
r_gen_planes_refined	0.01

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2281
Nucleic Acid Atoms
Solvent Atoms	355
Heterogen Atoms	60

Software

Software
Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction