9IAQ | pdb_00009iaq

Arbitrium controls lysis-lysogeny through the activation of a small antirepressor protein in the majority of arbitrium-coding phages

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3QQ6

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		291	16% PEG 4000, 10% 2-propanol, 100mM Hepes pH 7.5, 200mM ammonium sulfate

Crystal Properties
Matthews coefficient	Solvent content
2.09	41.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 37.873	α = 90
b = 85.778	β = 96.963
c = 84.164	γ = 90

Symmetry
Space Group	P 1 21 1

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 6M		2023-06-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALBA BEAMLINE XALOC	0.979257	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	1.89	42.889	99.8	0.048	0.019	0.999	21.4	7		42489

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.893	1.926			0.307	0.86	2.1

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	1.893	42.889	42487	2077	99.793	0.196	0.1938	0.1939	0.2288	0.2288	44.861

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]
0.787		2.241	-1.806		0.458

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.74
r_dihedral_angle_3_deg	13.521
r_dihedral_angle_2_deg	8.394
r_lrange_it	8.181
r_lrange_other	8.181
r_scangle_it	6.86
r_scangle_other	6.43
r_dihedral_angle_1_deg	6.284
r_scbond_it	4.881
r_scbond_other	4.452
r_mcangle_it	4.223
r_mcangle_other	4.222
r_mcbond_it	3.315
r_mcbond_other	3.314
r_angle_refined_deg	1.953
r_angle_other_deg	0.775
r_nbd_refined	0.21
r_nbtor_refined	0.169
r_symmetry_xyhbond_nbd_refined	0.156
r_symmetry_nbd_other	0.15
r_ncsr_local_group_3	0.149
r_ncsr_local_group_1	0.147
r_xyhbond_nbd_refined	0.146
r_ncsr_local_group_4	0.143
r_ncsr_local_group_6	0.141
r_symmetry_nbd_refined	0.134
r_ncsr_local_group_5	0.12
r_nbd_other	0.107
r_chiral_restr	0.106
r_ncsr_local_group_2	0.105
r_symmetry_nbtor_other	0.071
r_bond_refined_d	0.011
r_gen_planes_refined	0.01
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3651
Nucleic Acid Atoms
Solvent Atoms	147
Heterogen Atoms	55

Software

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