1XQH

Crystal structure of a ternary complex of the methyltransferase SET9 (also known as SET7/9) with a P53 peptide and SAH

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1O9S

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	7.8	291	PEG3350, Tris-HCL, pH 7.8, VAPOR DIFFUSION, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.46	49.68

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 40.374	α = 90
b = 103.123	β = 90.04
c = 67.165	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 4		2003-05-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SRS BEAMLINE PX14.2	0.978	SRS	PX14.2

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	1.75	20	94.7	0.038	24.8	15	55234	52283	3	3	27.7

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)
	1.75	1.81	67.6		0.378	2.5		3706

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	1o9s	1.75	20	52262	49595	2667	94.72	0.18571	0.18371	0.23	0.22325	0.25	RANDOM	7.381

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]
-1.62		0.65	0.28		1.34

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	17.846
r_dihedral_angle_1_deg	4.536
r_scangle_it	2.314
r_angle_refined_deg	1.753
r_angle_other_deg	1.732
r_scbond_it	1.429
r_mcangle_it	1.058
r_sphericity_free	0.952
r_rigid_bond_restr	0.887
r_sphericity_bonded	0.577
r_mcbond_it	0.551
r_nbtor_other	0.292
r_nbd_refined	0.268
r_symmetry_vdw_refined	0.243
r_nbd_other	0.241
r_symmetry_vdw_other	0.233
r_symmetry_hbond_refined	0.215
r_xyhbond_nbd_refined	0.182
r_chiral_restr	0.166
r_xyhbond_nbd_other	0.078
r_symmetry_hbond_other	0.024
r_bond_refined_d	0.01
r_gen_planes_other	0.007
r_gen_planes_refined	0.006
r_bond_other_d
r_dihedral_angle_2_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_metal_ion_refined
r_metal_ion_other
r_mcbond_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4002
Nucleic Acid Atoms
Solvent Atoms	717
Heterogen Atoms	52

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing