5U5K | pdb_00005u5k

Crystal structure of EED in complex with 3-(3-methoxybenzyl)piperidine hydrochloride

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	EVAPORATION		291	Crystals grown in a precipitant composed of 3-3.5 M sodium formate using the vapor diffusion method. Crystals grew in 3-5 days at 18 Celsius and harvested and soaked in defined drops consisting of 30 uL of precipitant with 1-2 mM of compound (typically solubilized in DMSO) for 24-48 h. Crystals were cryopreserved for data collection using a cryosolution consisting of 3.5 M sodium formate, 1-2 mM of compound, and 30% (v/v) glycerol.

Crystal Properties
Matthews coefficient	Solvent content
2.33	47.12

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 50.661	α = 90
b = 60.833	β = 104.56
c = 66.055	γ = 90

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	270	IMAGE PLATE	RIGAKU RAXIS IV		2016-04-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU FR-E SUPERBRIGHT	1.5418

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	44.71	93.2	19.2	6.1		15667			55.52

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 (Depositor)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION		THROUGHOUT	2.33	44.07	15618	764	93.1	0.166	0.163	0.225	0.2022	RANDOM	52.32

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]
0.9165		-0.2645	-0.0271		-0.8895

RMS Deviations
Key	Refinement Restraint Deviation
t_other_torsion	19.09
t_omega_torsion	3.58
t_angle_deg	1.17
t_bond_d	0.01
t_dihedral_angle_d
t_incorr_chiral_ct
t_pseud_angle
t_trig_c_planes
t_gen_planes
t_it
t_nbd
t_improper_torsion
t_chiral_improper_torsion
t_sum_occupancies
t_utility_distance
t_utility_angle
t_utility_torsion
t_ideal_dist_contact

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2853
Nucleic Acid Atoms
Solvent Atoms	155
Heterogen Atoms	18

Software

Software
Software Name	Purpose
BUSTER	refinement
XDS	data reduction
Aimless	data scaling
AMoRE	phasing