1TDZ

Crystal Structure Complex Between the Lactococcus Lactis FPG (Mutm) and a FAPY-dG Containing DNA

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	293	hepes, sodium citrate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
3.37	63.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 91.408	α = 90
b = 91.408	β = 90
c = 141.575	γ = 90

Symmetry
Space Group	P 41 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	ADSC QUANTUM 4			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-2	0.9330	ESRF	ID14-2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	1.8	76.7	99.3	0.048	8.7	3.6	55781	55781			24.879

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.8	1.9	100		0.234	3.1	3.6	8083

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1NNJ	1.8	20	52844	52844	2825	99.07	0.18034	0.18034	0.17891	0.20697	RANDOM	28.788

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]
-0.02			-0.02		0.03

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	5.737
r_scangle_it	4.122
r_scbond_it	2.62
r_mcangle_it	1.755
r_angle_refined_deg	1.709
r_mcbond_it	0.989
r_nbd_refined	0.21
r_symmetry_hbond_refined	0.178
r_xyhbond_nbd_refined	0.143
r_symmetry_vdw_refined	0.131

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	5.737
r_scangle_it	4.122
r_scbond_it	2.62
r_mcangle_it	1.755
r_angle_refined_deg	1.709
r_mcbond_it	0.989
r_nbd_refined	0.21
r_symmetry_hbond_refined	0.178
r_xyhbond_nbd_refined	0.143
r_symmetry_vdw_refined	0.131
r_chiral_restr	0.109
r_bond_refined_d	0.018
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2110
Nucleic Acid Atoms	569
Solvent Atoms	431
Heterogen Atoms	7

Software

Software
Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
AMoRE	phasing
REFMAC	refinement
CCP4	data scaling

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.