6V41

crystal structure of CDY1 chromodomain bound to H3K9me3

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	291	1.4 M sodium citrate, 0.1 M HEPES

Crystal Properties
Matthews coefficient	Solvent content
1.81	32.09

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 42.447	α = 90
b = 42.447	β = 90
c = 37.195	γ = 90

Symmetry
Space Group	P 43

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	RIGAKU SATURN A200		2014-09-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU FR-E	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	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	1.6	23.36	99.9	0.028	0.03	1	43.4	7		8814

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.6	1.63		99.1	0.371	0.403	0.914		6.6

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 (All)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	pdb entry 4hae	1.603	23.301	8794	411	99.955	0.193	0.1917	0.215	22.062

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]
0.253			0.253		-0.505

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.417
r_dihedral_angle_3_deg	15.351
r_dihedral_angle_4_deg	13.818
r_dihedral_angle_1_deg	6.416
r_lrange_it	4.516
r_lrange_other	4.457
r_scangle_it	2.7
r_scangle_other	2.698
r_angle_refined_deg	2.005
r_mcangle_it	1.937
r_mcangle_other	1.925
r_scbond_it	1.771
r_scbond_other	1.769
r_angle_other_deg	1.491
r_mcbond_it	1.323
r_mcbond_other	1.321
r_nbd_refined	0.282
r_symmetry_nbd_refined	0.239
r_nbd_other	0.229
r_symmetry_nbd_other	0.208
r_symmetry_xyhbond_nbd_refined	0.184
r_nbtor_refined	0.168
r_xyhbond_nbd_refined	0.092
r_chiral_restr	0.091
r_symmetry_nbtor_other	0.083
r_bond_refined_d	0.013
r_gen_planes_refined	0.009
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	586
Nucleic Acid Atoms
Solvent Atoms	20
Heterogen Atoms	20

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing