2V5I | pdb_00002v5i

Structure of the receptor-binding protein of bacteriophage Det7: a podoviral tailspike in a myovirus

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1TSP	PDB ENTRY 1TSP

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		4.5		10 TO 30 % (W/V) PEG4000, 0.1 M SODIUM CITRATE PH 4.5, 0 TO 15 % (V/V) GLYCEROL

Crystal Properties
Matthews coefficient	Solvent content
2.7	54

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 100.433	α = 90
b = 100.433	β = 90
c = 330.042	γ = 120

Symmetry
Space Group	H 3 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	IMAGE PLATE	MARRESEARCH	SILICON TOROIDAL MIRROR	2004-09-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-1		ESRF	ID23-1

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	1.6	15	94.6	0.08	13.1	5.2		80189			14.48

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	1.6	1.69	85.9		0.25	3.8	4.8

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 Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1TSP	1.6	15	78590	1598	94.6	0.142	0.141	0.15	0.17	RANDOM	13.12

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]
0.95	0.48		0.95		-1.43

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.123
r_dihedral_angle_4_deg	13.375
r_dihedral_angle_3_deg	12.264
r_dihedral_angle_1_deg	6.587
r_scangle_it	5.61
r_scbond_it	3.666
r_mcangle_it	2.434
r_angle_refined_deg	1.655
r_mcbond_it	1.418
r_angle_other_deg	0.888
r_symmetry_vdw_other	0.215
r_nbd_refined	0.196
r_nbd_other	0.183
r_nbtor_refined	0.169
r_symmetry_vdw_refined	0.151
r_symmetry_hbond_refined	0.143
r_xyhbond_nbd_refined	0.132
r_chiral_restr	0.121
r_nbtor_other	0.08
r_bond_refined_d	0.018
r_gen_planes_refined	0.009
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4143
Nucleic Acid Atoms
Solvent Atoms	831
Heterogen Atoms	1

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
AMoRE	phasing