6W0V | pdb_00006w0v

The Crystal Structure of the Mutant Nuclease Domain of Pyocin S8 with its Cognate Immunity Protein

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	291.15	Sodium Acetate 0.2M, PEG 4000 30%, Tris-HCl 0.1M pH 8.0

Crystal Properties
Matthews coefficient	Solvent content
1.8	31.58

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 42.178	α = 90
b = 47.071	β = 90
c = 99.86	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	80	PIXEL	DECTRIS PILATUS 2M		2017-10-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	LNLS BEAMLINE W01B-MX2	1.458660	LNLS	W01B-MX2

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	1.38	30	89.6	0.038	0.012	1	30.4	9		37296

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	1.38	1.4	32.1		0.403	0.296	0.795	1.7	1.7

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 (Depositor)	R-Free (Depositor)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	4UHP	1.381	29.983	37245	1793	89.413	0.18	0.1781	0.212	20.364

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]
-0.417			-1.337		1.754

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.207
r_dihedral_angle_4_deg	13.597
r_dihedral_angle_3_deg	12.887
r_rigid_bond_restr	12.356
r_dihedral_angle_1_deg	6.801
r_lrange_it	2.564
r_lrange_other	2.44
r_scangle_it	1.985
r_scangle_other	1.985
r_mcangle_it	1.93
r_mcangle_other	1.929
r_angle_other_deg	1.687
r_scbond_it	1.631
r_scbond_other	1.63
r_mcbond_it	1.58
r_mcbond_other	1.579
r_angle_refined_deg	1.452
r_symmetry_nbd_other	0.213
r_nbd_refined	0.208
r_nbd_other	0.205
r_xyhbond_nbd_other	0.203
r_symmetry_xyhbond_nbd_refined	0.2
r_nbtor_refined	0.188
r_symmetry_nbd_refined	0.174
r_xyhbond_nbd_refined	0.126
r_symmetry_nbtor_other	0.071
r_chiral_restr	0.063
r_bond_other_d	0.018
r_bond_refined_d	0.01
r_gen_planes_refined	0.007
r_gen_planes_other	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1629
Nucleic Acid Atoms
Solvent Atoms	213
Heterogen Atoms

Software

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