6RNZ

Crystal structure of the N-terminal HTH DNA-binding domain of the essential repressor DdrO from radiation-resistant Deinococcus bacteria (Deinococcus deserti)

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	0.1 M Bis-Tris propane pH 7, 2.5 M Ammonium Sulfate

Crystal Properties
Matthews coefficient	Solvent content
2.42	49.14

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 38.257	α = 90
b = 43.227	β = 106.66
c = 45.87	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	100	PIXEL	DECTRIS PILATUS3 2M		2016-07-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE MASSIF-1	0.9660	ESRF	MASSIF-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	1.35	44	98.3	0.048	10.9	2.8		31092

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.35	1.4

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	6RNX	1.35	43.94	29520	1558	98.2	0.13114	0.1287	0.17701	RANDOM	16.675

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]
0.26		-0.31	-0.23		0.13

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_free	38.979
r_dihedral_angle_2_deg	31.905
r_dihedral_angle_4_deg	23.005
r_dihedral_angle_3_deg	13.594
r_sphericity_bonded	12.856
r_long_range_B_refined	6.156
r_long_range_B_other	6.154
r_rigid_bond_restr	5.473
r_scangle_other	4.55
r_dihedral_angle_1_deg	4.242
r_scbond_other	3.903
r_scbond_it	3.897
r_angle_refined_deg	2.375
r_mcangle_it	1.909
r_mcangle_other	1.909
r_mcbond_it	1.694
r_mcbond_other	1.69
r_angle_other_deg	1.477
r_chiral_restr	0.159
r_bond_refined_d	0.029
r_gen_planes_refined	0.013
r_gen_planes_other	0.005
r_bond_other_d	0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1054
Nucleic Acid Atoms
Solvent Atoms	255
Heterogen Atoms	18

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
autoPROC	data scaling
MOLREP	phasing