2NMV

Damage detection by the UvrABC pathway: Crystal structure of UvrB bound to fluorescein-adducted DNA

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2D7D	PDB ENTRY 2D7D

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		8.5	289	18-20% PEG 20000, 0.1M pH 8.5 Tris-Hcl, microbatch, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
2.11	41.74

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 74.41	α = 90
b = 95.597	β = 90
c = 97.878	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	ADSC QUANTUM 4	Bent cylindrical mirror	2005-12-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-2	0.980	ESRF	ID23-2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2.95	68.36	99.1	0.094	0.094	15.9	5.3		15109	2	2	73.7

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.95	3.03	99.3		0.369	0.369	5.2	5.5	1087

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 2D7D	2.95	68.36	15109	14309	755	98.83	0.22706	0.22706	0.22428	0.28074	RANDOM	48.348

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]
1.21			-2.04		0.82

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.008
r_dihedral_angle_3_deg	20.405
r_dihedral_angle_4_deg	18.861
r_dihedral_angle_1_deg	6.527
r_scangle_it	3.052
r_scbond_it	1.799
r_angle_refined_deg	1.713
r_mcangle_it	1.234
r_mcbond_it	0.696
r_nbtor_refined	0.323

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.008
r_dihedral_angle_3_deg	20.405
r_dihedral_angle_4_deg	18.861
r_dihedral_angle_1_deg	6.527
r_scangle_it	3.052
r_scbond_it	1.799
r_angle_refined_deg	1.713
r_mcangle_it	1.234
r_mcbond_it	0.696
r_nbtor_refined	0.323
r_nbd_refined	0.246
r_symmetry_vdw_refined	0.243
r_symmetry_hbond_refined	0.181
r_xyhbond_nbd_refined	0.169
r_chiral_restr	0.101
r_bond_refined_d	0.016
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5179
Nucleic Acid Atoms	84
Solvent Atoms
Heterogen Atoms	48

Software

Software
Software Name	Purpose
REFMAC	refinement
ADSC	data collection
MOSFLM	data reduction
CCP4	data scaling
MOLREP	phasing

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.