4YEL | pdb_00004yel

Tailspike protein double mutant D339A/E372A of E. coli bacteriophage HK620 in complex with hexasaccharide

X-RAY DIFFRACTION

Starting Model(s)

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

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
2.17	43.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 74.36	α = 90
b = 74.36	β = 90
c = 174.679	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	CCD	RAYONIX MX-225	mirrors	2012-11-06	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	1.72	43.67	99.9	0.093	0.041	0.999	17.9	6		60326

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	1.72	1.75	97.6		0.763	0.345	0.729	2.3	5.8	3059

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	4AVZ	1.72	43.67	60326	3016	99.87	0.1368	0.135	0.15	0.1712	0.18	RANDOM	16.164

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]
0.32	0.16		0.32		-1.04

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.979
r_dihedral_angle_4_deg	15.932
r_dihedral_angle_3_deg	11.181
r_dihedral_angle_1_deg	7.261
r_angle_refined_deg	1.764
r_angle_other_deg	1.078
r_mcangle_it	0.972
r_mcbond_other	0.656
r_mcbond_it	0.655
r_chiral_restr	0.182

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.979
r_dihedral_angle_4_deg	15.932
r_dihedral_angle_3_deg	11.181
r_dihedral_angle_1_deg	7.261
r_angle_refined_deg	1.764
r_angle_other_deg	1.078
r_mcangle_it	0.972
r_mcbond_other	0.656
r_mcbond_it	0.655
r_chiral_restr	0.182
r_bond_refined_d	0.018
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	4516
Nucleic Acid Atoms
Solvent Atoms	763
Heterogen Atoms	113

Software

Software
Software Name	Purpose
XDS	data reduction
Aimless	data scaling
PHASER	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.