Experiment: 6M5M

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	10mM CaCl2, 10mM GlcNAc, 28% PEG 8000, 0.1M Tris-HCl (pH8.5), 0.2M sodium acetate, 10% glycerol

Crystal Properties
Matthews coefficient	Solvent content
2.41	49.05

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 44.46	α = 90
b = 44.46	β = 90
c = 303.613	γ = 120

Symmetry
Space Group	P 65

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 S 6M		2019-05-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE BL-5A	1.000	Photon Factory	BL-5A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.7	43.4	100	0.05	1	30	20.8		37198

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.7	1.73			0.91	0.942	3.3

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	6A7T	1.7	38.23	35272	1782	99.96	0.2037	0.203	0.2161	RANDOM	37.882

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.11
r_dihedral_angle_4_deg	14.672
r_dihedral_angle_3_deg	13.445
r_dihedral_angle_1_deg	7.413
r_angle_other_deg	2.585
r_angle_refined_deg	1.928
r_chiral_restr	0.134
r_bond_other_d	0.038
r_gen_planes_other	0.017
r_bond_refined_d	0.013

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.11
r_dihedral_angle_4_deg	14.672
r_dihedral_angle_3_deg	13.445
r_dihedral_angle_1_deg	7.413
r_angle_other_deg	2.585
r_angle_refined_deg	1.928
r_chiral_restr	0.134
r_bond_other_d	0.038
r_gen_planes_other	0.017
r_bond_refined_d	0.013
r_gen_planes_refined	0.011

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2193
Nucleic Acid Atoms
Solvent Atoms	139
Heterogen Atoms	34

Software

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