5JIN

Structure of G9a SET-domain with Histone H3K9M mutant peptide and bound S-adenosylmethionine

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2O8J

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	7	298	0.2 M Tri-ammonium citrate pH 7 and 20% w/v polyethylene glycol 3350

Crystal Properties
Matthews coefficient	Solvent content
2.46	50.05

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 56.434	α = 90
b = 78.684	β = 90.69
c = 72.769	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	178	CCD	ADSC QUANTUM 210		2013-01-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 14-BM-C	1.0010	APS	14-BM-C

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.85	72.76	98.4	14.87	3.8		50405

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	1.85	1.92	97.6		0.637	1.75	3.8

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2O8J	1.85	72.76	50405	2700	96.84	0.1993	0.19713	0.24	RANDOM	46.657

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]
-2.83		3.24	1.72		1.03

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.998
r_dihedral_angle_4_deg	15.7
r_dihedral_angle_3_deg	13.867
r_long_range_B_refined	9.261
r_long_range_B_other	9.259
r_scangle_other	7.376
r_dihedral_angle_1_deg	6.434
r_mcangle_other	5.482
r_mcangle_it	5.48
r_scbond_it	5.04
r_scbond_other	5.039
r_mcbond_it	4.098
r_mcbond_other	4.096
r_angle_refined_deg	1.757
r_angle_other_deg	1.298
r_chiral_restr	0.111
r_bond_refined_d	0.017
r_gen_planes_refined	0.01
r_bond_other_d	0.007
r_gen_planes_other	0.007
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	4488
Nucleic Acid Atoms
Solvent Atoms	249
Heterogen Atoms	62

Software

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