1XC8

CRYSTAL STRUCTURE COMPLEX BETWEEN THE WILD-TYPE 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	1TDZ	PDB ENTRY 1TDZ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	303	HEPES, SODIUM CITRATE, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 303K

Crystal Properties
Matthews coefficient	Solvent content
3.52	64.8

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 92.513	α = 90
b = 92.513	β = 90
c = 142.867	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	MARRESEARCH		2004-07-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE BM30A	0.92004	ESRF	BM30A

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	1.95	17.247	91.4	0.069	7.7		45806	41650

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	1.95	2.06	91.4		0.284	2.6	4.8	6134

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 1TDZ	1.95	17.247	39561	39561	2089	90.87	0.17805	0.17805	0.1764	0.20932	RANDOM	35.412

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]
0.33			0.33		-0.67

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.416
r_dihedral_angle_4_deg	17.948
r_dihedral_angle_3_deg	11.965
r_dihedral_angle_1_deg	5.971
r_scangle_it	3.962
r_scbond_it	2.727
r_angle_refined_deg	1.776
r_mcangle_it	1.745
r_mcbond_it	1.223
r_nbtor_refined	0.303

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.416
r_dihedral_angle_4_deg	17.948
r_dihedral_angle_3_deg	11.965
r_dihedral_angle_1_deg	5.971
r_scangle_it	3.962
r_scbond_it	2.727
r_angle_refined_deg	1.776
r_mcangle_it	1.745
r_mcbond_it	1.223
r_nbtor_refined	0.303
r_nbd_refined	0.211
r_symmetry_hbond_refined	0.207
r_xyhbond_nbd_refined	0.161
r_symmetry_vdw_refined	0.133
r_chiral_restr	0.119
r_bond_refined_d	0.02
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2128
Nucleic Acid Atoms	569
Solvent Atoms	397
Heterogen Atoms	7

Software

Software
Software Name	Purpose
Xnemo	data collection
SCALA	data scaling
AMoRE	phasing
REFMAC	refinement
XNEMO	data reduction
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.