5HLK

Crystal structure of the ternary EcoRV-DNA-Lu complex with cleaved DNA substrate.

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	293	9.4 mg/mL, 3:3 Enzyme:Well, 100 mM HEPES pH 7.5, 8% Ethylene glycol, 7% Polyethylene glycol 8000, 10% glycerol

Crystal Properties
Matthews coefficient	Solvent content
2.01	38.87

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 47.621	α = 96.94
b = 48.327	β = 108.78
c = 63.531	γ = 106.7

Symmetry
Space Group	P 1

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	RIGAKU SATURN 944		2014-01-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU FR-E DW	1.54178

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (Observed)	CC (Half)	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	1.95	58.46	78.9	0.051	0.057	0.995	20.3	4.3		28737		2	18.6

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.95	2	12		0.238	2.7	1.6

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1B94	2	40	26617	1365	82.95	0.16858	0.16553	0.22832	RANDOM	22.437

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]
0.37	-1.03	-0.79	2.48	-0.25	-1.28

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.576
r_dihedral_angle_4_deg	16.997
r_dihedral_angle_3_deg	15.107
r_dihedral_angle_1_deg	6.95
r_long_range_B_refined	6.616
r_long_range_B_other	6.614
r_scangle_other	4.002
r_mcangle_it	3.172
r_mcangle_other	3.171
r_scbond_it	2.463
r_scbond_other	2.46
r_mcbond_it	1.944
r_mcbond_other	1.944
r_angle_refined_deg	1.78
r_angle_other_deg	1.146
r_chiral_restr	0.116
r_bond_refined_d	0.016
r_gen_planes_refined	0.009
r_bond_other_d	0.002
r_gen_planes_other	0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4046
Nucleic Acid Atoms	468
Solvent Atoms	237
Heterogen Atoms	36

Software

Software
Software Name	Purpose
REFMAC	refinement
iMOSFLM	data reduction
SCALA	data scaling
PHASER	phasing