5GGD

Crystal structure of Mycobacterium smegmatis MutT1 in complex with phosphate and magnesium ions (excess magnesium, II)

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 magnesium chloride hexahydrate, 0.1 M TRIS hydrochloride, 30% w/v PEG 4000

Crystal Properties
Matthews coefficient	Solvent content
1.99	38.28

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 38.95	α = 90
b = 87.6	β = 100.06
c = 90.53	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		2014-10-06	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	1.7	44.57	99.9	6.6	3.2		65728

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	1.7	1.79	100		1.5	3.1

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	3FJY	1.7	44.57	62029	3313	99.38	0.21834	0.21614	0.25863	RANDOM	31.036

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]
-1.49		2.31	-3.21		3.66

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	27.339
r_dihedral_angle_4_deg	16.982
r_dihedral_angle_3_deg	15.019
r_dihedral_angle_1_deg	6.793
r_long_range_B_refined	6.73
r_long_range_B_other	6.604
r_scangle_other	4.906
r_mcangle_it	3.636
r_mcangle_other	3.636
r_scbond_it	3.315
r_scbond_other	3.303
r_mcbond_it	2.681
r_mcbond_other	2.674
r_angle_refined_deg	1.909
r_angle_other_deg	0.874
r_chiral_restr	0.111
r_bond_refined_d	0.017
r_gen_planes_refined	0.01
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	4556
Nucleic Acid Atoms
Solvent Atoms	511
Heterogen Atoms	16

Software

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