4YEJ | pdb_00004yej

Tailspike protein double mutant D339A/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 Sodiumformiate

Crystal Properties
Matthews coefficient	Solvent content
2.17	43.22

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 74.339	α = 90
b = 74.339	β = 90
c = 174.703	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	1.4	43.68	98	0.06	0.028	0.998	16.7	5.2		108242

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	1.4	1.43	80.3		0.528	0.36	0.685	1.9	2.4	4312

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	4XM3	1.4	43.68	108242	5413	97.9	0.1453	0.1439	0.15	0.1715	0.18	RANDOM	13.794

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]
0.06	0.03		0.06		-0.19

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.117
r_dihedral_angle_4_deg	17.477
r_dihedral_angle_3_deg	11.293
r_dihedral_angle_1_deg	7.663
r_angle_refined_deg	1.892
r_angle_other_deg	0.948
r_mcangle_it	0.912
r_mcbond_other	0.618
r_mcbond_it	0.614
r_chiral_restr	0.126

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4529
Nucleic Acid Atoms
Solvent Atoms	868
Heterogen Atoms	96

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.