4WQ4

E. coli YgjD(E12A)-YeaZ heterodimer in complex with ATP

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	0.1 M HEPES pH7.5, 25% PEG4000, 0.3 M Lithium Sulfate, 0.1 M Sodium Acetate

Crystal Properties
Matthews coefficient	Solvent content
2.43	49.35

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 63.27	α = 109.3
b = 68.07	β = 92.98
c = 87.13	γ = 117.23

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	173	PIXEL	DECTRIS PILATUS 6M		2013-12-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SOLEIL BEAMLINE PROXIMA 2	0.987	SOLEIL	PROXIMA 2

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	2.33	50	96.9	11.42	3.18		49021

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION		THROUGHOUT	2.33	49.04	46561	2451	97.08	0.20479	0.20229	0.25265	RANDOM	32.394

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]
0.55	0.47	0.52	0.81	0.3	-1.97

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.855
r_dihedral_angle_4_deg	14.907
r_dihedral_angle_3_deg	14.281
r_long_range_B_refined	6.264
r_long_range_B_other	6.264
r_dihedral_angle_1_deg	5.732
r_scangle_other	5.29
r_mcangle_it	4.271
r_mcangle_other	4.271
r_scbond_other	3.938
r_scbond_it	3.937
r_mcbond_it	3.116
r_mcbond_other	3.113
r_angle_refined_deg	1.454
r_angle_other_deg	0.851
r_chiral_restr	0.08
r_gen_planes_refined	0.015
r_bond_refined_d	0.014
r_gen_planes_other	0.011
r_bond_other_d	0.01
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	8337
Nucleic Acid Atoms
Solvent Atoms	282
Heterogen Atoms	92

Software

Software
Software Name	Purpose
REFMAC	refinement