7XW8 | pdb_00007xw8

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

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2Z5U

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	293	0.1 M imidazole-HCl (pH 6.5), 10% PEG 3350, 10% 2-methyl-2,4-pentanediol and 50 mM ammonium formate

Crystal Properties
Matthews coefficient	Solvent content
3.63	66.14

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 184.727	α = 90
b = 184.727	β = 90
c = 108.937	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		2014-12-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 5.0.2	0.97645	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	2.28	50	100	0.116	0.119	0.028	8.2	21.4		50185

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	2.28	2.32	100		0.339	0.927		20.3

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2Z5U	2.28	44.409	49937	2413	99.436	0.2	0.1981	0.2	0.2299	0.23	50.805

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]
1.279	0.639		1.279		-4.149

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.168
r_dihedral_angle_4_deg	17.992
r_dihedral_angle_3_deg	16.817
r_lrange_it	11.991
r_scangle_it	10.504
r_scbond_it	7.732
r_mcangle_it	7.418
r_dihedral_angle_1_deg	5.798
r_mcbond_it	5.701
r_angle_refined_deg	1.132

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.168
r_dihedral_angle_4_deg	17.992
r_dihedral_angle_3_deg	16.817
r_lrange_it	11.991
r_scangle_it	10.504
r_scbond_it	7.732
r_mcangle_it	7.418
r_dihedral_angle_1_deg	5.798
r_mcbond_it	5.701
r_angle_refined_deg	1.132
r_nbtor_refined	0.305
r_nbd_refined	0.198
r_symmetry_nbd_refined	0.15
r_symmetry_xyhbond_nbd_refined	0.146
r_xyhbond_nbd_refined	0.13
r_chiral_restr	0.085
r_gen_planes_refined	0.005
r_bond_refined_d	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5012
Nucleic Acid Atoms
Solvent Atoms	202
Heterogen Atoms	79

Software

Software
Software Name	Purpose
SCALEPACK	data scaling
MOLREP	phasing
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 R01GM157729.