5LBQ

LSD1-CoREST1 in complex with quinazoline-derivative reversible inhibitor

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2V1D

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	298	100 mM ADA pH 6.5 1.2 M Na/Ka Tartrate

Crystal Properties
Matthews coefficient	Solvent content
6.22	80.23

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 120.13	α = 90
b = 179.59	β = 90
c = 234.18	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	PIXEL	DECTRIS PILATUS 2M		2015-02-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06DA	1.000	SLS	X06DA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	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	3.3	99.85	100	0.191	0.943	5.7	5.3		38477

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	3.3	3.45	100		1.484	1.4	5.6

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2V1D	3.3	99.85	37697	751	99.86	0.23169	0.2313	0.23	0.24989	0.25	RANDOM	80.845

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]
5.33			-3.2		-2.13

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.687
r_dihedral_angle_3_deg	16.14
r_dihedral_angle_4_deg	15.38
r_long_range_B_refined	7.847
r_long_range_B_other	7.847
r_dihedral_angle_1_deg	6.159
r_mcangle_it	3.463
r_mcangle_other	3.463
r_scangle_other	3.149
r_mcbond_it	1.946
r_mcbond_other	1.943
r_scbond_it	1.707
r_scbond_other	1.707
r_angle_refined_deg	1.676
r_angle_other_deg	1.036
r_chiral_restr	0.079
r_bond_refined_d	0.011
r_gen_planes_refined	0.006
r_bond_other_d	0.003
r_gen_planes_other	0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
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
Heterogen Atoms	122

Software

Software
Software Name	Purpose
REFMAC	refinement
iMOSFLM	data reduction
Aimless	data scaling
PHASER	phasing