3JZN | pdb_00003jzn

Structure of EED in apo form

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5		3.5 mM NaF, 10 mM TCEP, 15% Glycerol, pH 7.5, VAPOR DIFFUSION, SITTING DROP

Crystal Properties
Matthews coefficient	Solvent content
2.65	53.58

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 57.64	α = 90
b = 85.159	β = 90
c = 91.327	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

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU	1.7

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.6	62.3	89.3		5.6	12902	12215

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	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	2.6	62.28	12215	650	89.33	0.17	0.17509	0.17162	0.17	0.23905	0.23	RANDOM	12.924

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]
0.36			-0.81		0.45

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.327
r_dihedral_angle_4_deg	20.275
r_dihedral_angle_3_deg	17.257
r_dihedral_angle_1_deg	6.611
r_scangle_it	3.77
r_scbond_it	2.222
r_angle_refined_deg	1.619
r_mcangle_it	1.415
r_mcbond_it	0.718
r_chiral_restr	0.11
r_bond_refined_d	0.016
r_gen_planes_refined	0.007
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2898
Nucleic Acid Atoms
Solvent Atoms	103
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement