2Q7U | pdb_00002q7u

Crystal Structure of the F plasmid TraI Relaxase Domain with the Scissile Thymidine Base and Imidodiphosphate

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1P4D	PDB entry 1p4d

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	298	protein buffer: 50 mM NaCl, 10% glycerol, 10 mM Tris-HCl pH 7.5, mother liquor: 75 mM sodium nitrate, 14% w/v PEG 3350, 10 mM spermine, 110 uM oriT DNA soaked (24 hours): 200 mM ammonium nitrate, 40% w/v PEG 3350, and 1 mM N,N-imidobisphosphonate (PNP), VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
1.84	33.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 44.5	α = 90
b = 86.31	β = 90
c = 127.91	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	MARMOSAIC 300 mm CCD		2006-02-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-B	0.97173	APS	23-ID-B

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	50	92.8	0.135	8.6	4.1	11257	10447			23

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	3.11	72.7		0.382		3.9

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 (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 1p4d	3	38.23	11257	9059	941	87.1	0.215	0.215	0.214	0.21	0.312	0.31	RANDOM	38.6

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]
-5.48			32.74		-27.26

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	22.5
c_scangle_it	4.42
c_scbond_it	2.68
c_mcangle_it	2.49
c_mcbond_it	1.4
c_angle_deg	1.2
c_improper_angle_d	0.82
c_bond_d	0.008
c_bond_d_na
c_bond_d_prot
c_angle_d
c_angle_d_na
c_angle_d_prot
c_angle_deg_na
c_angle_deg_prot
c_dihedral_angle_d_na
c_dihedral_angle_d_prot
c_improper_angle_d_na
c_improper_angle_d_prot

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4132
Nucleic Acid Atoms
Solvent Atoms	45
Heterogen Atoms	26

Software

Software
Software Name	Purpose
CNS	refinement
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing