2X6Y | pdb_00002x6y

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

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2VJI	PDB ENTRY 2VJI

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	293	VAPOR DIFFUSION, HANGING DROP:PROTEIN CONCENTRATION 8MG/ML. BUFFER: 40MM TRIS, PH7.8,2MM EDTA,0.2M NACL. RERVOIR: 100MM TRIS PH8.5,3.5M NA-FORMIATE. DROPLET 1.5:1.5 MICRO LITER, 0.3 MICRO LITER 33MM HEXASACCHARIDE. TEMPERATURE 20 DEGREE CELSIUS.

Crystal Properties
Matthews coefficient	Solvent content
2.14	42.48

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 74.336	α = 90
b = 74.336	β = 90
c = 174.977	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	GLAS MIRROR	2009-10-02	M	SINGLE WAVELENGTH

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

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.35	37.17	96.7	0.05	15.8	3.4		112857			17.6

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.35	1.39	58.5		0.34	2.6	2.3

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 2VJI	1.35	43.22	112857	5961	96.7	0.13406	0.13211	0.14	0.17074	0.18	RANDOM	13.8

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]
0.74	0.37		0.74		-1.1

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.681
r_dihedral_angle_4_deg	16.767
r_dihedral_angle_3_deg	10.996
r_dihedral_angle_1_deg	6.961
r_scangle_it	4.342
r_scbond_it	3.236
r_mcangle_it	2.077
r_mcbond_it	1.437
r_angle_refined_deg	1.327
r_rigid_bond_restr	1.145
r_angle_other_deg	0.885
r_mcbond_other	0.482
r_chiral_restr	0.084
r_bond_refined_d	0.01
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4529
Nucleic Acid Atoms
Solvent Atoms	693
Heterogen Atoms	82

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing