2DPD | pdb_00002dpd

Crystal structure of the Replication Termination Protein in complex with a pseudosymmetric B-site

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1F4K	PDB entry 1F4K with residues 71 to 89 of each monomer omitted

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.6	298	25% MPD, 75mM sodium acetate pH 4.6, 20mM calcium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
3.86	68.13

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 117.006	α = 90
b = 117.006	β = 90
c = 165.553	γ = 120

Symmetry
Space Group	P 64 2 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		2001-12-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 14-BM-C	1.00	APS	14-BM-C

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	3.15	60	97.5	0.069	23.2	6.5	12241	11638	1	1	57.1

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)
	3.15	3.25	91.6		0.365	3.3

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 1F4K with residues 71 to 89 of each monomer omitted	3.17	60	1	12241	11048	654	97.72	0.23835	0.23609	0.23	0.27781	0.28	RANDOM	96.207

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]
-2.87	-1.44		-2.87		4.31

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.637
r_dihedral_angle_3_deg	22.023
r_dihedral_angle_4_deg	19.069
r_dihedral_angle_1_deg	6.331
r_angle_refined_deg	1.718
r_nbtor_refined	0.324
r_symmetry_vdw_refined	0.28
r_nbd_refined	0.244
r_xyhbond_nbd_refined	0.177
r_chiral_restr	0.096

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.637
r_dihedral_angle_3_deg	22.023
r_dihedral_angle_4_deg	19.069
r_dihedral_angle_1_deg	6.331
r_angle_refined_deg	1.718
r_nbtor_refined	0.324
r_symmetry_vdw_refined	0.28
r_nbd_refined	0.244
r_xyhbond_nbd_refined	0.177
r_chiral_restr	0.096
r_bond_refined_d	0.013
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1939
Nucleic Acid Atoms	855
Solvent Atoms	12
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
ADSC	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 R01GM157729.