7E0G

Crystal structure of Lysine Specific Demethylase 1 (LSD1) with TAK-418, FAD-adduct

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	293	0.1 M imidazole/HCl (pH 7.0), 14% PEG 3350, 10% 2-methyl-2,4-pentanediol

Crystal Properties
Matthews coefficient	Solvent content
3.61	65.96

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 184.55	α = 90
b = 184.55	β = 90
c = 108.571	γ = 120

Symmetry
Space Group	P 61 2 2

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	ADSC QUANTUM 315r		2015-03-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 5.0.2	1.0	ALS	5.0.2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	2.25	159.82	99.7	0.08	0.079	0.025	9.2	13.4		51851

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.25	2.29	99.1		0.525	0.654		11.6

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	2Z5U	2.25	50	49246	2576	99.68	0.1957	0.1935	0.2382	RANDOM	60.134

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]
0.91	0.46		0.91		-2.96

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.198
r_dihedral_angle_4_deg	18.196
r_dihedral_angle_3_deg	15.619
r_dihedral_angle_1_deg	6.512
r_angle_refined_deg	1.129
r_chiral_restr	0.072
r_gen_planes_refined	0.009
r_bond_refined_d	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5022
Nucleic Acid Atoms
Solvent Atoms	208
Heterogen Atoms	73

Software

Software
Software Name	Purpose
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.