5HQ2 | pdb_00005hq2

Structural model of Set8 histone H4 Lys20 methyltransferase bound to nucleosome core particle

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	MICROBATCH	5.5	277	25 mM sodium acetate pH 5.5, 40 mM sodium citrate,1 mM DTT, 6% PEG2000-MME

Crystal Properties
Matthews coefficient	Solvent content
3.1	60.37

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 100.729	α = 90
b = 300.752	β = 90
c = 182.09	γ = 90

Symmetry
Space Group	C 2 2 21

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 315		2013-07-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 24-ID-E	0.9792	APS	24-ID-E

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	4.5	46.19	99.8	0.095	12.9	7.3	16854	16854

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	4.5	4.74	99.8		0.852	2.4	7.4

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	MOLECULAR REPLACEMENT	THROUGHOUT	4.5	46	15908	845	99.32	0.34184	0.33904	0.35	0.3972	0.4	RANDOM	171.987

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]
11.93			-7.31		-4.62

RMS Deviations
Key	Refinement Restraint Deviation
r_long_range_B_other	27.076
r_long_range_B_refined	27.075
r_mcangle_it	17.743
r_mcangle_other	17.743
r_scangle_other	16.727
r_scbond_it	10.886
r_scbond_other	10.885
r_mcbond_it	9.967
r_mcbond_other	9.951
r_dihedral_angle_1_deg	6.318
r_angle_other_deg	1.359
r_angle_refined_deg	0.99
r_chiral_restr	0.052
r_bond_refined_d	0.007
r_bond_other_d	0.004
r_gen_planes_refined	0.004
r_gen_planes_other	0.002
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
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	4767
Nucleic Acid Atoms	2971
Solvent Atoms
Heterogen Atoms

Software

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