8S3W | pdb_00008s3w

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, SITTING 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
2.08	40.91

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 44.27	α = 90
b = 60.87	β = 90
c = 124.68	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)	0.9790	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	2.39	99	99.8	0.186	0.194	0.996	9.94	13.2		13865

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	2.39	2.49			1.774	1.849	0.863	1.31

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	2.394	62.34	13865	664	99.791	0.19	0.1857	0.1961	0.2811	0.2836	63.36

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]
4.747			0.491		-5.238

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	17.459
r_dihedral_angle_6_deg	13.833
r_lrange_it	12.061
r_lrange_other	12.059
r_scangle_it	9.322
r_scangle_other	9.32
r_mcangle_other	8.236
r_mcangle_it	8.235
r_dihedral_angle_1_deg	8.167
r_dihedral_angle_2_deg	6.346
r_scbond_it	6.297
r_scbond_other	6.289
r_mcbond_it	5.668
r_mcbond_other	5.652
r_angle_refined_deg	1.689
r_angle_other_deg	0.57
r_xyhbond_nbd_refined	0.264
r_symmetry_nbd_refined	0.237
r_nbd_refined	0.228
r_symmetry_xyhbond_nbd_refined	0.224
r_nbd_other	0.218
r_symmetry_nbd_other	0.202
r_nbtor_refined	0.201
r_metal_ion_refined	0.122
r_symmetry_nbtor_other	0.086
r_chiral_restr	0.073
r_symmetry_xyhbond_nbd_other	0.009
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	2838
Nucleic Acid Atoms
Solvent Atoms	40
Heterogen Atoms	11

Software

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