Experiment: 4YJS

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
other		In-house SYK model

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.8	293	32.5% Jeffamine ED-2001, 10% Glycerol, 0.1M MES pH6.8, 5mM DTT

Crystal Properties
Matthews coefficient	Solvent content
1.95	36.8

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 38.407	α = 90
b = 84.617	β = 100.38
c = 39.756	γ = 90

Symmetry
Space Group	P 1 21 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	MAR CCD 130 mm		2005-03-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	OTHER	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2.22	28.712	100	0.059	0.059	18.7	3.7		12409

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	2.22	2.34	100		0.486	0.486	1.6	3.6	1802

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	THROUGHOUT	In-house SYK model	2.22	20	11790	598	99.92	0.1722	0.1696	0.2257	RANDOM	49.491

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]
1.35		-0.65			-1.57

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.685
r_dihedral_angle_4_deg	22.758
r_dihedral_angle_3_deg	13.691
r_dihedral_angle_1_deg	4.361
r_angle_refined_deg	1.444
r_angle_other_deg	0.892
r_chiral_restr	0.086
r_bond_refined_d	0.011
r_gen_planes_refined	0.005
r_bond_other_d	0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.685
r_dihedral_angle_4_deg	22.758
r_dihedral_angle_3_deg	13.691
r_dihedral_angle_1_deg	4.361
r_angle_refined_deg	1.444
r_angle_other_deg	0.892
r_chiral_restr	0.086
r_bond_refined_d	0.011
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2103
Nucleic Acid Atoms
Solvent Atoms	120
Heterogen Atoms	32

Software

Software
Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), 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 R01GM157729.