5AQ5 | pdb_00005aq5

Structure of the Carboxy-Terminal Domain of the Bacteriophage T5 L- Shaped Tail Fibre

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4UW7	PDB ENTRY 4UW7

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		8.5		0.1 M TRIS-HCL PH 8.5, 8% (W/V) PEG 4000, 10 MM IRON(III) CHLORIDE, 20% (V/V) GLYCEROL

Crystal Properties
Matthews coefficient	Solvent content
2.22	44.8

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 86.623	α = 68.24
b = 95.029	β = 70.2
c = 127.748	γ = 83.63

Symmetry
Space Group	P 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	PIXEL	DECTRIS PILATUS 6M	VERTICAL FOCUSING MIRROR AND HORIZONTAL FOCUSING MIRROR ORTHOGONAL IN A KIRKPATRICK-BAEZ CONFIGURATION	2014-12-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALBA BEAMLINE XALOC		ALBA	XALOC

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	2.3	23	91.3	0.08	7.6	2.4		144381

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	2.3	2.42	90.5		0.21	3	2.4

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 4UW7	2.3	23	140892	2906	90.87	0.22354	0.22297	0.22	0.25228	0.25	THIN SHELLS	62.601

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]
-0.66	2.03	-2.16	2.54	-1.05	-2.37

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.56
r_dihedral_angle_3_deg	12.454
r_dihedral_angle_4_deg	9.48
r_dihedral_angle_1_deg	7.128
r_angle_refined_deg	1.326
r_mcangle_it	1.044
r_scangle_it	1.038
r_scbond_it	0.62
r_mcbond_it	0.596
r_symmetry_vdw_refined	0.354
r_symmetry_hbond_refined	0.303
r_nbtor_refined	0.289
r_nbd_refined	0.167
r_xyhbond_nbd_refined	0.087
r_chiral_restr	0.08
r_bond_refined_d	0.009
r_gen_planes_refined	0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_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	24486
Nucleic Acid Atoms
Solvent Atoms	858
Heterogen Atoms

Software

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