9F5M | pdb_00009f5m

Structure of the C-terminal domain of bacteriophage K gp155, native

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	9F49

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	3	294	15% (w/v) PEG 8000, 83 mM MES-NaOH, 10 mM Tris-HCl

Crystal Properties
Matthews coefficient	Solvent content
3.06	59.75

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 76.13	α = 90
b = 43.334	β = 94.084
c = 98.982	γ = 90

Symmetry
Space Group	P 1 21 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		2018-11-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALBA BEAMLINE XALOC	0.97926	ALBA	XALOC

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	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	1.52	62.38	95.5	0.063	0.076	0.042	0.996	8.4	2.9		95840			22.2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.52	1.6			0.647	0.802	0.466	0.652	1.4

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.52	62.38	95832	4666	95.309	0.189	0.1881	0.1971	0.2131	0.2216	24.003

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]
0.392		0.743	-0.542		0.043

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.448
r_dihedral_angle_4_deg	13.436
r_dihedral_angle_3_deg	12.824
r_dihedral_angle_1_deg	6.665
r_lrange_it	5.474
r_lrange_other	5.219
r_scangle_it	3.276
r_scangle_other	3.275
r_mcangle_it	2.16
r_mcangle_other	2.16
r_scbond_it	2.071
r_scbond_other	2.071
r_mcbond_it	1.395
r_mcbond_other	1.394
r_angle_refined_deg	1.316
r_angle_other_deg	1.313
r_symmetry_nbd_refined	0.323
r_nbd_refined	0.194
r_symmetry_xyhbond_nbd_refined	0.179
r_symmetry_nbd_other	0.16
r_nbtor_refined	0.16
r_xyhbond_nbd_refined	0.142
r_nbd_other	0.124
r_symmetry_nbtor_other	0.074
r_chiral_restr	0.063
r_bond_refined_d	0.006
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3724
Nucleic Acid Atoms
Solvent Atoms	648
Heterogen Atoms	36

Software

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