2IW5 | pdb_00002iw5

Structural Basis for CoREST-Dependent Demethylation of Nucleosomes by the Human LSD1 Histone Demethylase

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.6	293	VAPOR DIFFUSION, SITTING DROP, 20 DEGREES. DROP: 0.8 MICRO-LITERS OF PROTEIN (10 MG/ML IN 25 MM HEPES, PH 7.4, 200 MM SODIUM CHLORIDE, 1 MM PMSF, 5 MM DTT) PLUS 0.8 MICRO-LITERS OF CRYSTALLIZATION SOLUTION (0.8 M LITHIUM SULFATE, 0.8 M AMMONIUM SULFATE, 0.4 M SODIUM CHLORIDE, 0.1 M SODIUM CITRATE, PH 5.6, 10 MM DTT). RESERVOIR: 1 ML OF CRYSTALLIZATION SOLUTION. CRYSTALS APPEARED WITHIN 12 HOURS AND GREW TO THEIR FINAL SIZE WITHIN 10 DAYS. CRYO-PROTECTION SOLUTION: RESERVOIR SOLUTION PLUS 23 PERCENT (V/V) GLYCEROL.

Crystal Properties
Matthews coefficient	Solvent content
6.2	80.1

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 120.354	α = 90
b = 178.222	β = 90
c = 234.932	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	CUSTOM		2006-03-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID		APS	19-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	2.57	49.87	93.3	0.06	39.3	9.3		75117		-3	70.3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.57	2.61	60.6		0.64	2	6.2

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	2.57	20	73416	1498	93.2	0.204	0.203	0.19	0.212	0.2	RANDOM	67.13

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]
3.11			-2.12		-0.99

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.224
r_dihedral_angle_4_deg	17.335
r_dihedral_angle_3_deg	16.993
r_dihedral_angle_1_deg	3.861
r_scangle_it	2.211
r_angle_refined_deg	1.448
r_scbond_it	1.35
r_mcangle_it	1.009
r_mcbond_it	0.599
r_nbtor_refined	0.308
r_nbd_refined	0.205
r_symmetry_vdw_refined	0.15
r_symmetry_hbond_refined	0.117
r_xyhbond_nbd_refined	0.104
r_chiral_restr	0.095
r_bond_refined_d	0.009
r_gen_planes_refined	0.007
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6293
Nucleic Acid Atoms
Solvent Atoms	78
Heterogen Atoms	69

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
SHELX	phasing