9TOY | pdb_00009toy

Investigating the binding mechanism of Interferon Regulatory Factor 4 to DNA in the context of Multiple Myeloma

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	PDB_00007OOT

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6	293	0.2M Calcium Acetate, 0.1M MES pH 6, 20% PEG 8000

Crystal Properties
Matthews coefficient	Solvent content
2.77	55.54

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 55.512	α = 89.859
b = 65.116	β = 75.316
c = 70.694	γ = 66.791

Symmetry
Space Group	P 1

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 EIGER2 XE 16M		2025-07-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.9762	Diamond	I03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	1.86	59.556	95.52	0.9757	11.14	3.6		70231

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.86	1.89			0.363

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	2.1	59.556	50135	1471	98.192	0.212	0.2107	0.2113	0.2578	0.2581	55.671

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]
6.724	0.12	-4.069	-4.995	0.131	-2.002

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	17.877
r_lrange_other	15.586
r_lrange_it	15.575
r_dihedral_angle_6_deg	15.052
r_scangle_it	11.962
r_scangle_other	11.961
r_dihedral_angle_2_deg	10.681
r_mcangle_it	9.853
r_mcangle_other	9.851
r_scbond_it	9.634
r_scbond_other	9.634
r_mcbond_it	8.011
r_mcbond_other	7.99
r_dihedral_angle_1_deg	7.469
r_angle_refined_deg	2.877
r_angle_other_deg	0.845
r_dihedral_angle_other_2_deg	0.815
r_symmetry_xyhbond_nbd_refined	0.34
r_nbd_other	0.244
r_nbd_refined	0.224
r_symmetry_nbd_refined	0.22
r_symmetry_nbd_other	0.217
r_nbtor_refined	0.217
r_xyhbond_nbd_refined	0.19
r_chiral_restr	0.126
r_ncsr_local_group_1	0.123
r_ncsr_local_group_4	0.119
r_ncsr_local_group_3	0.114
r_ncsr_local_group_8	0.111
r_symmetry_nbtor_other	0.098
r_ncsr_local_group_5	0.095
r_metal_ion_refined	0.084
r_ncsr_local_group_2	0.064
r_ncsr_local_group_6	0.05
r_ncsr_local_group_7	0.049
r_symmetry_xyhbond_nbd_other	0.043
r_gen_planes_refined	0.018
r_bond_refined_d	0.015
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3749
Nucleic Acid Atoms	1640
Solvent Atoms	107
Heterogen Atoms	5

Software

Software
Software Name	Purpose
REFMAC	refinement
xia2	data reduction
xia2	data scaling
PHASER	phasing