7Q4T

Structure of the Pseudomonas aeruginosa bacteriophage JG004 endolysin Pae87 bound to a peptidoglycan fragment.

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7Q4S

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8	294	0.12 M Tris-HCl, 20% (w/v) PEG 5000 MME, 8% (v/v) ethylene glycol

Crystal Properties
Matthews coefficient	Solvent content
2	38.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 43.581	α = 90
b = 61.173	β = 90
c = 69.21	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		2020-05-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALBA BEAMLINE XALOC	0.97933	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	1.27	69.21	99.9	0.042	0.046	0.018	1	17.6	6.4		49510			13.938

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	1.27	1.29	100		0.753	0.825	0.33	0.903	2	6

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 (All)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	7Q4S	1.27	45.854	49442	2454	99.81	0.132	0.1304	0.1608	21.016

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]
-0.729			0.137		0.592

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.452
r_dihedral_angle_4_deg	22.866
r_dihedral_angle_3_deg	11.083
r_dihedral_angle_1_deg	5.636
r_lrange_it	3.244
r_scangle_it	3.208
r_scangle_other	3.207
r_lrange_other	3.066
r_scbond_it	2.576
r_scbond_other	2.575
r_mcangle_it	1.951
r_mcangle_other	1.95
r_mcbond_it	1.671
r_mcbond_other	1.671
r_angle_other_deg	1.445
r_rigid_bond_restr	1.417
r_angle_refined_deg	1.361
r_symmetry_nbd_refined	0.249
r_nbd_refined	0.247
r_nbd_other	0.207
r_symmetry_nbd_other	0.177
r_nbtor_refined	0.173
r_symmetry_xyhbond_nbd_refined	0.165
r_xyhbond_nbd_refined	0.115
r_symmetry_nbtor_other	0.094
r_chiral_restr	0.077
r_bond_refined_d	0.007
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	1500
Nucleic Acid Atoms
Solvent Atoms	117
Heterogen Atoms	99

Software

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