4WRX

Crystal structure of Mycobacterium tuberculosis uracil-DNA glycosylase, Form V

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3A7N

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	MICROBATCH	5.6	293	Ammonium acetate, Sodium citrate tribasic dihydrate, PEG 4000

Crystal Properties
Matthews coefficient	Solvent content
2.05	40.03

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 36.89	α = 90
b = 45	β = 90
c = 122.61	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	MARMOSAIC 225 mm CCD		2013-12-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE BM14	0.97856	ESRF	BM14

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	1.4	40.87	99.5	0.081	10.3	5		40968

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.4	1.48	99		0.622	2.4	4.9

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	3A7N	1.4	40.87	38825	2054	99.33	0.1248	0.1236	0.14793	RANDOM	17.378

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]
1.01			-0.98		-0.04

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_free	53.583
r_dihedral_angle_2_deg	38.634
r_dihedral_angle_4_deg	17.698
r_sphericity_bonded	13.71
r_dihedral_angle_3_deg	11.914
r_long_range_B_refined	6.572
r_dihedral_angle_1_deg	5.992
r_scangle_other	5.162
r_rigid_bond_restr	5.061
r_long_range_B_other	4.951
r_scbond_it	4.573
r_scbond_other	4.561
r_mcangle_other	3.008
r_mcangle_it	3.005
r_mcbond_it	2.45
r_mcbond_other	2.442
r_angle_refined_deg	1.919
r_angle_other_deg	0.963
r_chiral_restr	0.138
r_bond_refined_d	0.019
r_gen_planes_refined	0.011
r_gen_planes_other	0.002
r_bond_other_d	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

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1750
Nucleic Acid Atoms
Solvent Atoms	321
Heterogen Atoms	3

Software

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