4XOT

Tailspike protein mutant E372Q of E. coli bacteriophage HK620 in complex with pentasaccharide

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4XM3

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	298	0.1 M Tris-HCl, 3.5 M Sodium formate

Crystal Properties
Matthews coefficient	Solvent content
2.16	42.92

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 74.179	α = 90
b = 74.179	β = 90
c = 174.678	γ = 120

Symmetry
Space Group	P 3 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	PIXEL	DECTRIS PILATUS 6M	mirrors	2014-01-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.1	0.91841	BESSY	14.1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.06	43.67	99.4	0.058	0.028	0.999	13.9	5.2		250525

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.06	1.08	89		0.62	0.357	0.694	2.1	3.7	10927

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	4XM3	1.06	43.67	250525	12512	99.27	0.1065	0.1053	0.1296	RANDOM	11.576

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]
0.27	0.13		0.27		-0.87

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.881
r_sphericity_free	35.774
r_dihedral_angle_4_deg	18.534
r_dihedral_angle_3_deg	10.658
r_sphericity_bonded	10.087
r_dihedral_angle_1_deg	7.658
r_rigid_bond_restr	6.01
r_angle_refined_deg	1.938
r_mcangle_it	1.788
r_mcbond_it	1.393

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.881
r_sphericity_free	35.774
r_dihedral_angle_4_deg	18.534
r_dihedral_angle_3_deg	10.658
r_sphericity_bonded	10.087
r_dihedral_angle_1_deg	7.658
r_rigid_bond_restr	6.01
r_angle_refined_deg	1.938
r_mcangle_it	1.788
r_mcbond_it	1.393
r_mcbond_other	1.392
r_angle_other_deg	0.978
r_chiral_restr	0.133
r_bond_refined_d	0.02
r_gen_planes_refined	0.011
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4532
Nucleic Acid Atoms
Solvent Atoms	852
Heterogen Atoms	103

Software

Software
Software Name	Purpose
XDS	data reduction
Aimless	data scaling
REFMAC	phasing
ARP	model building
Coot	model building
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.