1TDZ

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

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1NNJ	PDB ENTRY 1NNJ

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 U.S. National Science Foundation (DBI-2321666), 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 R01GM157729.