3ABT

Crystal Structure of LSD1 in complex with trans-2-pentafluorophenylcyclopropylamine

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2DW4	PDB ENTRY 2DW4

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	278	3-10% PEG 2000 Monomethyl ether, 0.1M Hepes pH 7.5, 0.2M magnesium chloride, 0.1M cacodylate, 5mM Tranylcypromine-derivative, VAPOR DIFFUSION, HANGING DROP, temperature 278K

Crystal Properties
Matthews coefficient	Solvent content
3.61	65.97

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 183.84	α = 90
b = 183.84	β = 90
c = 109.15	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 315		2008-04-15	M	SINGLE WAVELENGTH
2	1	x-ray	100	CCD	MARMOSAIC 225 mm CCD		2008-12-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL41XU	1.000000	SPring-8	BL41XU
2	SYNCHROTRON	SPRING-8 BEAMLINE BL26B2	1.000000	SPring-8	BL26B2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym I (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	3.2	50	99	0.226	9.77	8.7		18396

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	3.21	3.34	98.2		0.612	0.612	2.11	4.4	2820

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	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	PDB ENTRY 2DW4	3.2	47.73	2.1	18396	893	99.8	0.231	0.231	0.272	RANDOM	58.9

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]
9.78			9.78		-19.57

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	20.9
c_mcangle_it	1.07
c_angle_deg	0.9
c_scangle_it	0.86
c_improper_angle_d	0.7
c_mcbond_it	0.57
c_scbond_it	0.47
c_bond_d	0.003
c_bond_d_na
c_bond_d_prot
c_angle_d
c_angle_d_na
c_angle_d_prot
c_angle_deg_na
c_angle_deg_prot
c_dihedral_angle_d_na
c_dihedral_angle_d_prot
c_improper_angle_d_na
c_improper_angle_d_prot

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5049
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	68

Software

Software
Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
CNS	refinement
HKL-2000	data reduction
SCALEPACK	data scaling