2DW4 | pdb_00002dw4

Crystal structure of human LSD1 at 2.3 A resolution

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	277	4% PEGMME 2000, 100mM HEPES-Na, 5% MPD, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K

Crystal Properties
Matthews coefficient	Solvent content
3.63	66.1

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 184.31	α = 90
b = 184.31	β = 90
c = 108.768	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		2006-03-25	M	SINGLE WAVELENGTH

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

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	2.3	50	99.8				48471	-3	-3	27.6

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.3	2.38	98.7

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-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	2.3	33.74	44078	2278	90.7	0.192	0.192	0.19	0.226	0.18	RANDOM	46.3

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]
6.24	6.13		6.24		-12.48

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	22.5
c_scangle_it	7.63
c_scbond_it	5.88
c_mcangle_it	4.68
c_mcbond_it	3.47
c_angle_deg	1.4
c_improper_angle_d	0.96
c_bond_d	0.009
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	4968
Nucleic Acid Atoms
Solvent Atoms	294
Heterogen Atoms	53

Software

Software
Software Name	Purpose
CNS	refinement
ADSC	data collection
HKL-2000	data reduction
HKL-2000	data scaling
SOLVE	phasing