5V37 | pdb_00005v37

Crystal structure of SMYD3 with SAM and EPZ028862

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	293	0.10 M Magnesium formate, 0.1M Tris 8.0, 14% w/v PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.2	44.07

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 60.818	α = 90
b = 65.868	β = 90
c = 107.015	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	PIXEL	DECTRIS EIGER X 9M		2014-11-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-D	1.0	APS	21-ID-D

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	1.41	17.26	97.7	0.074	8.8	5.8		75322

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	1.42	1.45	85.9		0.346	2.6	4.1

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		THROUGHOUT	1.42	17.26	75322	3831	97.62	0.23	0.2276	0.2265	0.2789	0.2793	RANDOM	18.09

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]
-1.59			1.11		0.48

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.522
r_sphericity_free	26.83
r_dihedral_angle_3_deg	14.958
r_dihedral_angle_4_deg	14.943
r_sphericity_bonded	9.867
r_dihedral_angle_1_deg	5.722
r_rigid_bond_restr	4.713
r_angle_refined_deg	1.359
r_angle_other_deg	0.934
r_chiral_restr	0.077
r_bond_refined_d	0.008
r_gen_planes_refined	0.005
r_gen_planes_other	0.003
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3395
Nucleic Acid Atoms
Solvent Atoms	499
Heterogen Atoms	87

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
KYLIN	data reduction
KYLIN	data scaling