2DPU

Crystal structure of the replication termination protein in complex with a pseudosymmetric 21mer B-site DNA

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.6	298	1.75M ammonium sulfate, 0.1M sodium acetate pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.49	50.67

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 73.049	α = 90
b = 73.049	β = 90
c = 68.411	γ = 120

Symmetry
Space Group	P 62

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	IMAGE PLATE	MAR scanner 345 mm plate	mirrors	2000-06-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU200	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	3.1	40	99.5			3829	3807			63

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	3.1	3.18	98.9

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	3.1	40	1	3807	3636	170	99.5	0.2061	0.20199	0.30609	RANDOM	50.068

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]
-3.47	-1.73		-3.47		5.2

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	42.371
r_dihedral_angle_3_deg	20.32
r_dihedral_angle_4_deg	14.308
r_dihedral_angle_1_deg	4.115
r_angle_refined_deg	1.369
r_scangle_it	1.314
r_scbond_it	0.72
r_mcangle_it	0.572
r_nbtor_refined	0.304
r_mcbond_it	0.304

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	42.371
r_dihedral_angle_3_deg	20.32
r_dihedral_angle_4_deg	14.308
r_dihedral_angle_1_deg	4.115
r_angle_refined_deg	1.369
r_scangle_it	1.314
r_scbond_it	0.72
r_mcangle_it	0.572
r_nbtor_refined	0.304
r_mcbond_it	0.304
r_symmetry_vdw_refined	0.237
r_nbd_refined	0.219
r_xyhbond_nbd_refined	0.142
r_symmetry_hbond_refined	0.13
r_chiral_restr	0.059
r_bond_refined_d	0.008
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	961
Nucleic Acid Atoms	427
Solvent Atoms	8
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
MAR345	data collection
DENZO	data reduction
SCALEPACK	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 R01GM133198.