8I6C

Crystal structure of Mycobacterium tuberculosis Uracil-DNA glycosylase in complex with 6-Formyl-uracil, Form III

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4WRV

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	MICROBATCH		293	0.1 M Bis-Tris pH 5.5, 0.5 M Sodium citrate, 25% PEG (w/v) 3350

Crystal Properties
Matthews coefficient	Solvent content
2.03	39.35

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 46.51	α = 90
b = 59.92	β = 90
c = 75.14	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	IMAGE PLATE	RIGAKU RAXIS IV		2021-04-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU ULTRAX 18	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	2.28	39.55	98.29	0.0665	0.989	6.84	2		9957

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.28	2.362			0.3817	0.869

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	4WRV	2.28	39.58	9407	476	98.3	0.21228	0.20864	0.2792	RANDOM	22.864

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]
-0.81			0.35		0.46

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.406
r_dihedral_angle_4_deg	17.654
r_dihedral_angle_3_deg	13.134
r_dihedral_angle_1_deg	6.803
r_long_range_B_refined	5.556
r_long_range_B_other	5.506
r_scangle_other	3.609
r_mcangle_it	3.202
r_mcangle_other	3.202
r_angle_other_deg	2.342
r_scbond_other	2.211
r_scbond_it	2.206
r_mcbond_it	2.054
r_mcbond_other	2.038
r_angle_refined_deg	1.587
r_chiral_restr	0.069
r_bond_other_d	0.035
r_gen_planes_other	0.014
r_bond_refined_d	0.008
r_gen_planes_refined	0.008
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	1685
Nucleic Acid Atoms
Solvent Atoms	119
Heterogen Atoms	10

Software

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