2BQZ | pdb_00002bqz

Crystal structure of a ternary complex of the human histone methyltransferase Pr-SET7 (also known as SET8)

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		7		pH 7.00

Crystal Properties
Matthews coefficient	Solvent content
1.9	34.92

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 42.179	α = 64.74
b = 46.322	β = 86.66
c = 51.998	γ = 90.61

Symmetry
Space Group	P 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 CCD			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-2		ESRF	ID14-2

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	1.5	19.9	89.1	0.07	9.5	4.3		63273		2

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-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	OTHER	THROUGHOUT	1.5	20	50828	2663	94	0.188	0.187	0.206	RANDOM	13.44

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]
1.79	0.58	-0.1	-1.87	0.41	-0.24

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	16.125
r_dihedral_angle_1_deg	4.432
r_scangle_it	3.299
r_scbond_it	2.112
r_mcangle_it	1.58
r_angle_refined_deg	1.579
r_mcbond_it	0.893
r_angle_other_deg	0.722
r_symmetry_vdw_other	0.352
r_nbd_refined	0.322
r_symmetry_vdw_refined	0.267
r_symmetry_hbond_refined	0.258
r_nbd_other	0.229
r_xyhbond_nbd_refined	0.211
r_nbtor_other	0.139
r_chiral_restr	0.094
r_bond_refined_d	0.011
r_gen_planes_refined	0.006
r_gen_planes_other	0.003
r_bond_other_d	0.001
r_dihedral_angle_2_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2774
Nucleic Acid Atoms
Solvent Atoms	613
Heterogen Atoms	50

Software

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