Experiment: 3SYK

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	6.5	291	0.4 M (NH4)2SO4, 0.05 M MES-NaOH pH 6.5, vapor diffusion, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.75	55.26

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 76.77	α = 90
b = 93.993	β = 90
c = 106.964	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	CCD	ADSC QUANTUM 315r		2009-12-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-1	0.97915	ESRF	ID23-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	3.081	43.883	99.2	0.064	13.1	3.6	14768	14768

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3.08	3.25	95.2		0.322	0.322	2.4	3.6	2023

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	3.08	20	13915	13915	752	100	0.2229	0.2197	0.2832	RANDOM	56.1304

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]
0.09			0.2		-0.3

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.242
r_dihedral_angle_3_deg	19.599
r_dihedral_angle_4_deg	17.826
r_dihedral_angle_1_deg	4.837
r_scangle_it	1.611
r_angle_refined_deg	1.076
r_scbond_it	1.039
r_mcangle_it	0.791
r_mcbond_it	0.459
r_nbtor_refined	0.302

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.242
r_dihedral_angle_3_deg	19.599
r_dihedral_angle_4_deg	17.826
r_dihedral_angle_1_deg	4.837
r_scangle_it	1.611
r_angle_refined_deg	1.076
r_scbond_it	1.039
r_mcangle_it	0.791
r_mcbond_it	0.459
r_nbtor_refined	0.302
r_nbd_refined	0.201
r_symmetry_vdw_refined	0.178
r_xyhbond_nbd_refined	0.127
r_symmetry_hbond_refined	0.119
r_chiral_restr	0.068
r_bond_refined_d	0.007
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4305
Nucleic Acid Atoms
Solvent Atoms	23
Heterogen Atoms	30

Software

Software
Software Name	Purpose
SCALA	data scaling
SHELX	phasing
RESOLVE	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data scaling
XDS	data reduction
SHELXD	phasing

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.