Experiment: 6YO7

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.8	291	1.6 M sodium citrate, 50 mM Tris-H2SO4

Crystal Properties
Matthews coefficient	Solvent content
2.04	39.77

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 41.719	α = 90
b = 41.033	β = 103.7
c = 71.716	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	PIXEL	DECTRIS PILATUS3 6M		2019-04-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.1	0.9184	BESSY	14.1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim 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	1.17	35.36	94.2	0.048	0.057	0.999	12.05	3.525		75212			17.258

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.17	1.24	72.7		0.809	1.035	0.516	1.01	2.464

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	5OGP	1.17	35.36	73111	2100	94.27	0.1604	0.1597	0.1848	RANDOM	16.799

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]
-1.68		-0.76	0.62		1.28

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.839
r_rigid_bond_restr	21.453
r_sphericity_free	21.189
r_dihedral_angle_4_deg	18.62
r_sphericity_bonded	12.461
r_dihedral_angle_3_deg	11.061
r_dihedral_angle_1_deg	6.867
r_angle_other_deg	4.357
r_angle_refined_deg	1.665
r_chiral_restr	0.109

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.839
r_rigid_bond_restr	21.453
r_sphericity_free	21.189
r_dihedral_angle_4_deg	18.62
r_sphericity_bonded	12.461
r_dihedral_angle_3_deg	11.061
r_dihedral_angle_1_deg	6.867
r_angle_other_deg	4.357
r_angle_refined_deg	1.665
r_chiral_restr	0.109
r_bond_refined_d	0.014
r_gen_planes_refined	0.011
r_gen_planes_other	0.009
r_bond_other_d	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2008
Nucleic Acid Atoms
Solvent Atoms	236
Heterogen Atoms	27

Software

Software
Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
FFT	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.