6BHD | pdb_00006bhd

Crystal structure of SETDB1 with a modified H3 peptide

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		similar, nearly isomorphous crystal structure, to be published

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	7.5	291	25% PEG3350, 0.2 M sodium chloride, 0.1 M HEPES, 5% glycerol

Crystal Properties
Matthews coefficient	Solvent content
2.32	47.01

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 37.258	α = 90
b = 72.448	β = 104.84
c = 52.505	γ = 90

Symmetry
Space Group	P 1 21 1

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 315r		2013-08-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.9686	APS	19-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim 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	1.25	41.57	99.8	0.05	0.059	0.03	0.999	15.1	3.7		74273

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.25	1.27	99.8		1.018	1.198	0.625	0.487		3.6	3645

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)	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	THROUGHOUT	similar, nearly isomorphous crystal structure, to be published	1.25	41.57	70524	3722	99.8	0.1492	0.1474	0.16	0.1829	0.19	16.006

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]
-0.17		-0.06	0.32		-0.1

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.886
r_sphericity_free	19.119
r_dihedral_angle_4_deg	17.305
r_dihedral_angle_3_deg	12.186
r_sphericity_bonded	8.964
r_dihedral_angle_1_deg	6.949
r_mcangle_it	4.028
r_mcbond_it	3.228
r_mcbond_other	3.224
r_rigid_bond_restr	2.955
r_angle_refined_deg	1.937
r_angle_other_deg	1.106
r_chiral_restr	0.127
r_bond_refined_d	0.019
r_gen_planes_refined	0.011
r_bond_other_d	0.003
r_gen_planes_other	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1805
Nucleic Acid Atoms
Solvent Atoms	203
Heterogen Atoms	36

Software

Software
Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
REFMAC	phasing