Experiment: 5YG3

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	MICROBATCH	8.5	298	PEG 4000, 0.06-0.12 M NaCl, 0.1 M Tris-HCl pH 8.5

Crystal Properties
Matthews coefficient	Solvent content
2.38	48.42

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 101.623	α = 90
b = 58.727	β = 90.32
c = 236.139	γ = 90

Symmetry
Space Group	C 1 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	CMOS	BRUKER PHOTON 100		2017-07-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	BRUKER D8 QUEST	1.54

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	2.4	19.81	96.1	0.09	0.097	0.037	0.998	14.8	6.5		52746

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	2.4	2.47	96.5		0.381	0.439	0.211	0.948		3.8

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	4TMR	2.4	19.81	47271	5468	95.78	0.2301	0.2222	0.3	RANDOM	38.325

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]
2.72		-0.17	2.65		-5.36

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.058
r_dihedral_angle_3_deg	18.748
r_dihedral_angle_4_deg	16.119
r_dihedral_angle_1_deg	6.165
r_angle_refined_deg	1.603
r_angle_other_deg	1.008
r_chiral_restr	0.082
r_bond_refined_d	0.011
r_gen_planes_refined	0.006
r_bond_other_d	0.002

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.058
r_dihedral_angle_3_deg	18.748
r_dihedral_angle_4_deg	16.119
r_dihedral_angle_1_deg	6.165
r_angle_refined_deg	1.603
r_angle_other_deg	1.008
r_chiral_restr	0.082
r_bond_refined_d	0.011
r_gen_planes_refined	0.006
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10374
Nucleic Acid Atoms
Solvent Atoms	239
Heterogen Atoms	152

Software

Software
Software Name	Purpose
Aimless	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
PHASER	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.