9SF2 | pdb_00009sf2

Phage Phi106 repressor in complex with AimX

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		294	20% PEG 3350, 100mM Zinc Acetate, 100mM imidazole pH8

Crystal Properties
Matthews coefficient	Solvent content
2.25	45.22

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 56.991	α = 90
b = 56.991	β = 90
c = 100.716	γ = 90

Symmetry
Space Group	P 43 21 2

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		2025-05-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALBA BEAMLINE XALOC	0.97926	ALBA	XALOC

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Rpim I (All)	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	1.7	49.601	100	0.012	35.1	25		19015

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rpim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.7	1.79	100		0.077	9.1	26.2

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	1.7	49.601	18942	976	99.937	0.181	0.1787	0.1789	0.2187	0.2187	42.297

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]
-0.58			-0.58		1.16

RMS Deviations
Key	Refinement Restraint Deviation
r_lrange_it	24.076
r_lrange_other	24.07
r_scangle_it	19.06
r_scangle_other	19.05
r_dihedral_angle_6_deg	17.148
r_mcangle_it	15.425
r_mcangle_other	15.419
r_scbond_it	14.386
r_scbond_other	14.376
r_dihedral_angle_3_deg	14.208
r_mcbond_it	11.669
r_mcbond_other	11.353
r_dihedral_angle_2_deg	6.201
r_rigid_bond_restr	5.893
r_dihedral_angle_1_deg	5.079
r_angle_refined_deg	1.724
r_angle_other_deg	0.785
r_nbd_refined	0.212
r_symmetry_nbd_refined	0.196
r_nbd_other	0.195
r_xyhbond_nbd_refined	0.185
r_nbtor_refined	0.164
r_symmetry_nbd_other	0.152
r_symmetry_xyhbond_nbd_refined	0.125
r_chiral_restr	0.095
r_symmetry_nbtor_other	0.065
r_symmetry_metal_ion_refined	0.062
r_bond_refined_d	0.01
r_gen_planes_refined	0.007
r_bond_other_d	0.003
r_gen_planes_other	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1220
Nucleic Acid Atoms
Solvent Atoms	67
Heterogen Atoms	39

Software

Software
Software Name	Purpose
SCALA	data scaling
gemmi	data extraction
REFMAC	refinement
XDS	data reduction
MOLREP	phasing