9SIM | pdb_00009sim

Phage epsilon15 tailspike gp20 containing domains beta-helix, beta-sandwich and petal domains

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5LW3
experimental model	PDB	9SIJ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	294	0.1 M Tris-HcL pH 7.5, 3 M Na-formate

Crystal Properties
Matthews coefficient	Solvent content
3.61	65.94

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 117.326	α = 90
b = 117.326	β = 90
c = 251.291	γ = 120

Symmetry
Space Group	H 3

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		2018-11-29	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)	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	1.94	83.904	96.3	0.998	10.3	5.1		92011			29.276066

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.94	2.04	75.6		0.647	1.6	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	MOLECULAR REPLACEMENT	THROUGHOUT	1.94	83.904	92009	4737	96.318	0.16	0.1592	0.163	0.1782	0.182	32.057

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]
-0.253	-0.126		-0.253		0.82

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	13.929
r_dihedral_angle_3_deg	9.981
r_dihedral_angle_1_deg	6.822
r_dihedral_angle_2_deg	5.161
r_lrange_it	4.612
r_lrange_other	4.422
r_scangle_it	2.241
r_scangle_other	2.241
r_mcangle_it	1.662
r_mcangle_other	1.662
r_scbond_it	1.349
r_scbond_other	1.349
r_mcbond_it	0.986
r_mcbond_other	0.986
r_angle_refined_deg	0.88
r_angle_other_deg	0.342
r_nbd_refined	0.189
r_symmetry_nbd_other	0.184
r_nbtor_refined	0.168
r_symmetry_nbd_refined	0.166
r_nbd_other	0.146
r_xyhbond_nbd_refined	0.123
r_metal_ion_refined	0.106
r_symmetry_xyhbond_nbd_refined	0.103
r_symmetry_nbtor_other	0.077
r_chiral_restr	0.045
r_gen_planes_refined	0.003
r_bond_refined_d	0.002
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6305
Nucleic Acid Atoms
Solvent Atoms	714
Heterogen Atoms	77

Software

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