3DLM | pdb_00003dlm

Crystal structure of Tudor domain of human Histone-lysine N-methyltransferase SETDB1

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	293	1.5 microliter of the protein solution was mixed with 1.5 microliter of the reservoir solution containing 0.2 M Disodium tartrate, 20% PEG 3350 and 0.1M Hepes pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.41	51.61

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 54.518	α = 90
b = 63.689	β = 90
c = 69.083	γ = 90

Symmetry
Space Group	P 21 21 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	IMAGE PLATE	RIGAKU RAXIS IV		2008-06-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU FR-E+ DW	1.54178

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	1.77	50	99.7	0.049	42.6	6.9		24050

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)
	1.77	1.83	99.6		0.178		6.6	2357

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	SAD	THROUGHOUT	1.77	46.83	23997	1223	99.63	0.21	0.208	0.2039	0.237	0.232	RANDOM	27.003

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]
0.49			-0.64		0.15

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.56
r_dihedral_angle_4_deg	20.649
r_dihedral_angle_3_deg	12.735
r_dihedral_angle_1_deg	6.28
r_scangle_it	3.408
r_scbond_it	2.444
r_mcangle_it	1.567
r_angle_refined_deg	1.369
r_mcbond_it	0.99
r_nbtor_refined	0.308
r_nbd_refined	0.223
r_symmetry_vdw_refined	0.17
r_xyhbond_nbd_refined	0.12
r_symmetry_hbond_refined	0.104
r_chiral_restr	0.1
r_bond_refined_d	0.013
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1702
Nucleic Acid Atoms
Solvent Atoms	212
Heterogen Atoms

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
SHELXD	phasing