8S3M | pdb_00008s3m

LysTt72, a lytic endopeptidase from Thermus thermophilus MAT72 phage vB_Tt72

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6JMY

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	293	20% v/v PEG 500 MME, 10% w/v PEG 20000, 30 mM sodium nitrate, 30 mM sodium phosphate dibasic, 30 mM ammonium sulfate, 0.1 M 6.5 imidazole/MES monohydrate (acid) at pH 6.5

Crystal Properties
Matthews coefficient	Solvent content
2.12	42.03

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 44.133	α = 90
b = 60.985	β = 90
c = 125.342	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-F	focussing mirrors	2023-08-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1)	0.7749	PETRA III, EMBL c/o DESY	P13 (MX1)

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym I (Observed)	Rrim 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	2.198	15	99.2	0.243	0.264	0.994	8.36	6.5		17755

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.198	2.33	98.4		1.478	1.602	0.726	1.65	6.6

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)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.198	14.956	17755	930	99.223	0.191	0.1874	0.2005	0.2598	0.2686	Random	41.393

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]
4.192			-1.167		-3.025

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	17.887
r_dihedral_angle_6_deg	13.779
r_lrange_other	8.641
r_lrange_it	8.64
r_dihedral_angle_1_deg	7.771
r_dihedral_angle_2_deg	7.36
r_scangle_it	6.849
r_scangle_other	6.847
r_mcangle_other	5.652
r_mcangle_it	5.648
r_scbond_it	4.41
r_scbond_other	4.389
r_mcbond_it	3.717
r_mcbond_other	3.717
r_angle_refined_deg	1.641
r_angle_other_deg	0.571
r_symmetry_xyhbond_nbd_refined	0.26
r_nbd_other	0.236
r_symmetry_nbd_refined	0.226
r_nbd_refined	0.217
r_symmetry_nbd_other	0.207
r_nbtor_refined	0.193
r_xyhbond_nbd_refined	0.184
r_metal_ion_refined	0.142
r_symmetry_nbtor_other	0.087
r_chiral_restr	0.078
r_symmetry_xyhbond_nbd_other	0.014
r_gen_planes_refined	0.008
r_bond_refined_d	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	2796
Nucleic Acid Atoms
Solvent Atoms	65
Heterogen Atoms	53

Software

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