Experiment: 5YSW

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	8.5	277	Magnesium chloride hexahydrate, PEG 4000

Crystal Properties
Matthews coefficient	Solvent content
2.16	42.93

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 35.082	α = 90
b = 70.709	β = 94
c = 80.975	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	SIEMENS-NICOLET	mirrors	2017-11-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL19U1	0.976	SSRF	BL19U1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	2.55	50	98.7	0.11	0.12	0.049	5.7	5.8		12806

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	2.55	2.64	99.3		0.555	0.609	0.247	0.833		5.7

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	MOLECULAR REPLACEMENT	THROUGHOUT	4OQS	2.6	35.38	11248	580	96.22	0.2085	0.2052	0.2714	RANDOM	37.57

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]
0.33		0.19	-0.59		0.24

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.69
r_dihedral_angle_4_deg	26.466
r_dihedral_angle_3_deg	22.456
r_dihedral_angle_1_deg	6.278
r_angle_refined_deg	1.704
r_angle_other_deg	0.924
r_chiral_restr	0.099
r_bond_refined_d	0.013
r_gen_planes_refined	0.009
r_bond_other_d	0.005

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.69
r_dihedral_angle_4_deg	26.466
r_dihedral_angle_3_deg	22.456
r_dihedral_angle_1_deg	6.278
r_angle_refined_deg	1.704
r_angle_other_deg	0.924
r_chiral_restr	0.099
r_bond_refined_d	0.013
r_gen_planes_refined	0.009
r_bond_other_d	0.005
r_gen_planes_other	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2868
Nucleic Acid Atoms
Solvent Atoms	64
Heterogen Atoms	97

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data scaling
PDB_EXTRACT	data extraction
HKL-3000	data reduction
REFMAC	phasing

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 R01GM133198.