Experiment: 4XBF

Structure of LSD1:CoREST in complex with ssRNA

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2IW5

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.6	290	The LSD1-CoREST complex 10-12 mg/ml concentration (in 25 mM HEPES-Na, pH 7.4, 100 mM NaCl, 5 mM DTT, 1 mM PMSF) was mixed (1:1) with the reservoir solution [0.60 M Li2SO4, 0.63 M (NH4)2SO4, 0.25 M NaCl, 100 mM Na-citrate, pH 5.6, 10 mM DTT]

Crystal Properties
Matthews coefficient	Solvent content
	80

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 121.073	α = 90
b = 178.411	β = 90
c = 234.676	γ = 90

Symmetry
Space Group	I 2 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	MARMOSAIC 225 mm CCD	12.7 KeV energy range, focused beam size: 50uM x 50uM	2014-07-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-F	0.97872	APS	21-ID-F

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	2.803	49.018	99.5	0.037	23.8	14.6	62563	62270

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.803	2.8732	96.8			12.5

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2IW5	2.803	49.018	1.35	62268	2000	99.55	0.202	0.2011	0.2032	0.2268	0.2287	62.8

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]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	14.966
f_angle_d	0.743
f_chiral_restr	0.027
f_plane_restr	0.004
f_bond_d	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6293
Nucleic Acid Atoms	86
Solvent Atoms	23
Heterogen Atoms	84

Software

Software
Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
Coot	model building