5F8A | pdb_00005f8a

Crystal structure of the ternary EcoRV-DNA-Lu complex with uncleaved DNA substrate. Lanthanide binding to EcoRV-DNA complex inhibits cleavage.

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1B95

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.4	285	4.5 mg/mL (monomer), protein(dimer):DNA - 1:1, Enzyme:Well - 3uL:3uL, Well - 500uL of 100 mM HEPES pH 7.4, 8% Ethylene glycol, 4% Polyethylene glycol 8000, 10% glycerol.

Crystal Properties
Matthews coefficient	Solvent content
2.24	45.18

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 46.43	α = 70.61
b = 52.86	β = 73.24
c = 65.31	γ = 81.81

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	IMAGE PLATE	RIGAKU RAXIS HTC		2015-11-18	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)	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	1.76	36.673	93	0.051	0.059	14.7	3.9		51697			21.698

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	1.76	1.85	88.9		0.196	4.4	3.2

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	1B95	1.76	36.673	46685	5000	92.94	0.16402	0.16026	0.17	0.19914	0.21	RANDOM	27.868

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]
0.96	-0.78	0.85	1.36	-0.66	-1.83

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.752
r_dihedral_angle_4_deg	20.122
r_dihedral_angle_3_deg	14.434
r_dihedral_angle_1_deg	6.598
r_long_range_B_refined	6.468
r_long_range_B_other	6.468
r_scangle_other	5.393
r_scbond_it	3.806
r_scbond_other	3.806
r_mcangle_other	3.521
r_mcangle_it	3.52
r_mcbond_it	2.672
r_mcbond_other	2.666
r_angle_refined_deg	1.574
r_angle_other_deg	1.056
r_chiral_restr	0.103
r_bond_refined_d	0.017
r_gen_planes_refined	0.009
r_bond_other_d	0.007
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	486
Solvent Atoms	301
Heterogen Atoms	12

Software

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