3DTK

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

X-RAY DIFFRACTION

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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
2.25	45.25

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 87.26	α = 90
b = 52.672	β = 90
c = 63.221	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 4			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-2	0.93300	ESRF	ID14-2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	3.24	40	97.7	0.095	13.1	4.5		4827			89

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	3.24	3.42	97.9		0.598	2.2	4.7

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 3DTE	3.24	19.83	4581	222	96.82	0.22853	0.22627	0.27702	RANDOM	75.982

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]
0.04			-0.12		0.08

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.009
r_dihedral_angle_3_deg	17.24
r_dihedral_angle_4_deg	14.23
r_dihedral_angle_1_deg	4.469
r_angle_refined_deg	0.867
r_mcangle_it	0.801
r_mcbond_it	0.732
r_angle_other_deg	0.673
r_scangle_it	0.399
r_scbond_it	0.314
r_symmetry_vdw_other	0.265
r_nbd_refined	0.257
r_nbd_other	0.219
r_symmetry_hbond_refined	0.213
r_xyhbond_nbd_refined	0.197
r_nbtor_refined	0.19
r_symmetry_vdw_refined	0.165
r_nbtor_other	0.093
r_xyhbond_nbd_other	0.082
r_mcbond_other	0.058
r_chiral_restr	0.048
r_bond_refined_d	0.007
r_gen_planes_refined	0.002
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	1873
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	3

Software

Software
Software Name	Purpose
REFMAC	refinement
DNA	data collection
MOSFLM	data reduction
SCALA	data scaling