9F49 | pdb_00009f49

Structure of the bacteriophage K gp155 C-terminal domain, seleno-methionine modified version

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	294	20% (w/v)PEG 1500, 100 mM HEPES-NaOH pH 7.5, 10 mM Tris-HCl

Crystal Properties
Matthews coefficient	Solvent content
2.08	40.84

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 42.397	α = 90
b = 42.861	β = 90
c = 123.646	γ = 90

Symmetry
Space Group	P 21 21 21

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		2018-09-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALBA BEAMLINE XALOC	0.97872	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	1.62	123.65	89.4	0.089	0.093	0.027	0.998	20.9	10.7		26390			17.6

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	1.62	1.71	56.1		0.471	0.529	0.232	0.729	3.2	5

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	SAD	THROUGHOUT	1.621	61.823	26329	1266	89.387	0.159	0.1582	0.158	0.1837	0.1831	18.598

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]
0.426			-0.102		-0.324

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.642
r_dihedral_angle_4_deg	17.529
r_dihedral_angle_3_deg	10.73
r_dihedral_angle_1_deg	6.731
r_lrange_it	4.236
r_lrange_other	4.054
r_scangle_it	2.662
r_scangle_other	2.647
r_scbond_it	1.691
r_scbond_other	1.68
r_mcangle_other	1.65
r_mcangle_it	1.647
r_angle_other_deg	1.326
r_angle_refined_deg	1.319
r_mcbond_it	1.031
r_mcbond_other	1.019
r_nbd_refined	0.194
r_nbd_other	0.168
r_symmetry_nbd_other	0.165
r_nbtor_refined	0.163
r_xyhbond_nbd_refined	0.143
r_symmetry_xyhbond_nbd_refined	0.12
r_symmetry_nbd_refined	0.114
r_metal_ion_refined	0.098
r_symmetry_xyhbond_nbd_other	0.096
r_symmetry_nbtor_other	0.072
r_chiral_restr	0.059
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	1862
Nucleic Acid Atoms
Solvent Atoms	210
Heterogen Atoms	21

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
CRANK2	phasing