2QNC | pdb_00002qnc

Crystal structure of T4 Endonuclease VII N62D mutant in complex with a DNA Holliday junction

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		T4 ENDONUCLEASE VII-HETERODUPLEX COMPLEX

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		5.5	293	25 %(w/v) PEG 3350, 0.1 M Bis-Tris, pH 5.5, VAPOR DIFFUSION, temperature 293K, pH 5.50

Crystal Properties
Matthews coefficient	Solvent content
3.49	64.77

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 99.197	α = 90
b = 99.197	β = 90
c = 186.884	γ = 90

Symmetry
Space Group	P 43 21 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		2003-06-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-1		ESRF	ID14-1

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	3.1	42.27	98.9	0.066	26.8	7.9		17475			77.1

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)
	3.1	3.22	95.7		0.66	3.73	7.3

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 (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	T4 ENDONUCLEASE VII-HETERODUPLEX COMPLEX	3.1	42.27	17612	17475	703	99.2	0.258	0.258	0.25	0.278	0.28	RANDOM	102.7

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]

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	19.6
c_scangle_it	2.36
c_mcangle_it	1.75
c_scbond_it	1.4
c_angle_deg	1.2
c_improper_angle_d	1.11
c_mcbond_it	1
c_bond_d	0.009
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	2544
Nucleic Acid Atoms	1893
Solvent Atoms	11
Heterogen Atoms	12

Software

Software
Software Name	Purpose
CNS	refinement
XDS	data reduction
XDS	data scaling
XSCALE	data scaling
PHASER	phasing