2FDC

Structural Basis of DNA Damage Recognition and Processing by UvrB: crystal structure of a UvrB/DNA complex

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.5	293	20mM MgCl2, 14% PEG3000, 80mM sodium citrate pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
3.32	62.91

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 153.265	α = 90
b = 153.265	β = 90
c = 160.17	γ = 120

Symmetry
Space Group	P 32 2 1

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		2005-11-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X26C	1.1	NSLS	X26C

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	3.3	50	99.9	0.138		7.8	33350	33350	2	2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3.3	3.42	100		0.548		7.9	3332

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	3.3	10	33350	31873	1580	100	0.207	0.21	0.205	0.258	RANDOM	71.961

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]
1.97	0.98		1.97		-2.95

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.248
r_dihedral_angle_3_deg	16.42
r_dihedral_angle_4_deg	14.052
r_dihedral_angle_1_deg	4.078
r_mcangle_it	2.626
r_scangle_it	2.174
r_mcbond_it	1.613
r_angle_refined_deg	1.37
r_scbond_it	1.255
r_angle_other_deg	0.796
r_mcbond_other	0.229
r_nbd_refined	0.209
r_symmetry_vdw_other	0.189
r_nbtor_refined	0.182
r_nbd_other	0.18
r_symmetry_hbond_refined	0.149
r_xyhbond_nbd_refined	0.147
r_symmetry_vdw_refined	0.11
r_nbtor_other	0.085
r_chiral_restr	0.082
r_xyhbond_nbd_other	0.069
r_bond_refined_d	0.019
r_bond_other_d	0.003
r_gen_planes_refined	0.003
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8803
Nucleic Acid Atoms	343
Solvent Atoms
Heterogen Atoms	32

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
AMoRE	phasing