4XOR | pdb_00004xor

Tailspike protein double mutant D339N/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	42.99

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 74.257	α = 90
b = 74.257	β = 90
c = 174.512	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	1.5	43.14	99.9	0.073	0.032	0.999	18.4	6		90151

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	1.5	1.53	98		0.743	0.364	0.731	2.1	5.1	4325

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	1.5	43.14	90151	4504	99.95	0.1438	0.1425	0.15	0.1685	0.18	RANDOM	15.108

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]
0.19	0.1		0.19		-0.63

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.337
r_dihedral_angle_4_deg	16.845
r_dihedral_angle_3_deg	11.345
r_dihedral_angle_1_deg	7.445
r_angle_refined_deg	1.795
r_mcangle_it	0.96
r_angle_other_deg	0.916
r_mcbond_it	0.668
r_mcbond_other	0.668
r_chiral_restr	0.125

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.337
r_dihedral_angle_4_deg	16.845
r_dihedral_angle_3_deg	11.345
r_dihedral_angle_1_deg	7.445
r_angle_refined_deg	1.795
r_mcangle_it	0.96
r_angle_other_deg	0.916
r_mcbond_it	0.668
r_mcbond_other	0.668
r_chiral_restr	0.125
r_bond_refined_d	0.019
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	746
Heterogen Atoms	98

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.