5HNK | pdb_00005hnk

Crystal structure of T5Fen in complex intact substrate and metal ions.

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1EXN

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.5	290	The concentration of both oligonucleotides was adjusted to 1.1 mM for the duplex molecule by dissolving each one in 10 mM MES pH 6.5 and 50 mM KCl. They were annealed by heating to 367K for 10 minutes and allowed to cool to room temperature. Crystals with oligonucleotide 5ov4 were grown at 290K with the D153K variant of T5Fen. The resulting T5FenD153K:5ov4 structure was determined from crystals grown in 0.2 M MgCl2, 0.1 M Bis-Tris buffer pH 5.5, 25% w/v PEG 3350.

Crystal Properties
Matthews coefficient	Solvent content
2.24	45.06

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 44.72	α = 90
b = 109.94	β = 90
c = 127.34	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	PIXEL	DECTRIS PILATUS 6M	Please check which detector was in place at that date	2011-04-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I24	0.977	Diamond	I24

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym I (Observed)	Rrim I (All)	Rpim I (All)	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	2.22	44.72	99.4	0.079	0.094	0.038	13.4	5.7	31727	31727

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Rpim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.22	2.28	94.8		0.654	0.654	0.405	0.9	3.1	2177

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	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	1EXN	2.22	42.19	30073	1595	99.35	0.1851	0.1826	0.1869	0.2344	0.2344	RANDOM	48.335

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]
-0.17			-0.46		0.63

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.873
r_dihedral_angle_3_deg	11.925
r_dihedral_angle_4_deg	11.084
r_dihedral_angle_1_deg	5.305
r_mcangle_it	3.997
r_mcbond_it	2.659
r_mcbond_other	2.659
r_angle_refined_deg	1.066
r_angle_other_deg	0.947
r_chiral_restr	0.065
r_bond_refined_d	0.007
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4407
Nucleic Acid Atoms	490
Solvent Atoms	224
Heterogen Atoms	9

Software

Software
Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
xia2	data reduction
PHASER	phasing