6M65 | pdb_00006m65

Crystal structure of Mycobacterium smegmatis MutT1 in complex with GMPPNP (GDP)

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
2.1	41.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 192.56	α = 90
b = 37.11	β = 90
c = 44.79	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	1.44	43.63	99.7	0.086	0.092	0.034	0.998	12.3	7.1		59223

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	1.44	1.52	99.7		0.75	0.75	0.809	0.302	1	7

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	1.44	36.76	56131	2985	99.51	0.1831	0.1814	0.1823	0.2148	0.2152	RANDOM	16.954

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]
-0.62			-0.05		0.66

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	26.285
r_dihedral_angle_4_deg	20.43
r_dihedral_angle_3_deg	12.939
r_dihedral_angle_1_deg	6.416
r_angle_other_deg	2.375
r_angle_refined_deg	2.08
r_chiral_restr	0.108
r_bond_other_d	0.034
r_bond_refined_d	0.018
r_gen_planes_other	0.017
r_gen_planes_refined	0.012

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2258
Nucleic Acid Atoms
Solvent Atoms	441
Heterogen Atoms	64

Software

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