8P8E | pdb_00008p8e

Crystal structure of endolysin gp46 from Pseudomonas aeruginosa bacteriophage vB_PaeM_KTN6

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4OK7

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		294	10 mM HEPES-NaOH pH 7.0; 10 mM trisodium citrate; 16% (w/v) PEG 6000

Crystal Properties
Matthews coefficient	Solvent content
2.37	48.05

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 41.796	α = 90
b = 43.201	β = 90
c = 126.181	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		2017-09-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALBA BEAMLINE XALOC	0.97929	ALBA	XALOC

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.39	43.2	99.9	0.059	0.026	0.999	15.8	6.4		46757			17.995

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.39	1.47	99.7		1.002	0.425	0.695	1.8	6.4

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	FREE R-VALUE	1.391	40.003	46682	2227	99.767	0.128	0.1263	0.13	0.1641	0.17	27.118

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]
-0.292			0.645		-0.353

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.048
r_dihedral_angle_4_deg	20.032
r_dihedral_angle_3_deg	11.992
r_dihedral_angle_1_deg	6.376
r_lrange_it	4.688
r_scangle_it	4.432
r_scangle_other	4.43
r_lrange_other	4.394
r_scbond_it	3.673
r_scbond_other	3.671
r_mcangle_it	2.942
r_mcangle_other	2.941
r_mcbond_it	2.363
r_mcbond_other	2.357
r_rigid_bond_restr	1.76
r_angle_other_deg	1.457
r_angle_refined_deg	1.419
r_nbd_other	0.258
r_symmetry_nbd_refined	0.241
r_nbd_refined	0.211
r_symmetry_nbd_other	0.17
r_nbtor_refined	0.167
r_xyhbond_nbd_refined	0.145
r_symmetry_xyhbond_nbd_refined	0.102
r_chiral_restr	0.078
r_symmetry_nbtor_other	0.077
r_bond_refined_d	0.008
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1686
Nucleic Acid Atoms
Solvent Atoms	234
Heterogen Atoms	25

Software

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