3DTI

Crystal structure of the IRRE protein, a central regulator of DNA damage repair in deinococcaceae

X-RAY DIFFRACTION

---

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	7.5	281	20% PEG 3350, 0.2M Potassium fluoride, pH 7.5, VAPOR DIFFUSION, temperature 281K

Crystal Properties
Matthews coefficient	Solvent content
2.31	46.74

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 88.19	α = 90
b = 53.41	β = 90
c = 63.42	γ = 90

Symmetry
Space Group	P 21 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	CCD	ADSC QUANTUM 315			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID29	0.97618	ESRF	ID29

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (Observed)	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	3.5	40	99.4	0.102	0.077	8.1	3.5		4071			63

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	3.5	3.69	99.4		0.48	0.364	2	3.6	579

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 3DTE	3.5	20	3842	181	99.16	0.24451	0.24131	0.23	0.3142	0.3	RANDOM	66.089

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]
3.02			-4.09		1.07

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.675
r_dihedral_angle_3_deg	19.353
r_dihedral_angle_4_deg	10.656
r_dihedral_angle_1_deg	6.18
r_angle_refined_deg	1.073
r_mcangle_it	1.047
r_mcbond_it	0.917
r_angle_other_deg	0.706
r_scangle_it	0.54
r_scbond_it	0.407
r_nbd_refined	0.282
r_xyhbond_nbd_refined	0.262
r_nbd_other	0.23
r_symmetry_vdw_other	0.208
r_nbtor_refined	0.198
r_symmetry_hbond_refined	0.177
r_symmetry_vdw_refined	0.167
r_xyhbond_nbd_other	0.129
r_nbtor_other	0.094
r_mcbond_other	0.074
r_chiral_restr	0.051
r_bond_refined_d	0.01
r_gen_planes_refined	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1838
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	1

Software

Software
Software Name	Purpose
REFMAC	refinement
DNA	data collection
XDS	data reduction
SCALA	data scaling
deduced	phasing