5T5G | pdb_00005t5g

human SETD8 in complex with MS2177

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4IJ8

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION		291	30% PEG-2000-MME, 0.1 M postassium thiocyanate, 0.1 M Bis-Tris

Crystal Properties
Matthews coefficient	Solvent content
2.38	48.35

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 88.957	α = 90
b = 88.957	β = 90
c = 34.989	γ = 120

Symmetry
Space Group	P 32 2 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 315r		2014-07-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.97918	APS	19-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	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	2.1	44.48	99.9	0.081	0.085	0.026	0.999	19.8	10.7		9530

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.1	2.16	100		0.985	1.033	0.309	0.856	3.1	11.1	775

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	4ij8	2.1	44.48	8998	519	99.87	0.2061	0.2049	0.2136	0.2273	0.2374	52.152

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]
0.78	0.39		0.78		-2.54

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.465
r_dihedral_angle_4_deg	14.145
r_dihedral_angle_3_deg	12.832
r_dihedral_angle_1_deg	6.39
r_mcangle_it	3.053
r_mcbond_it	2.096
r_mcbond_other	2.057
r_angle_refined_deg	1.485
r_angle_other_deg	0.917
r_chiral_restr	0.084
r_bond_refined_d	0.014
r_gen_planes_refined	0.006
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1072
Nucleic Acid Atoms
Solvent Atoms	19
Heterogen Atoms	49

Software

Software
Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
XDS	data scaling
PHASER	phasing