8R7Y | pdb_00008r7y

Deoxyribonucleoside regulator DeoR in complex with the DNA operator

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4OQQ	for residues 56-313
experimental model	PDB	2W48	for residues 1-55

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.3	292	The volume ratio of the protein/DNA solution and precipitant solution - 1:2 Precipitant solution: 50 mM sodium cacodylate, pH 6.3, 75 mM CaCl2, 25 mM MgCl2, 3.5% (v/v) PEG 2K Crystal was cryo-protected by a quick soaking in 25% (v/v) glycerol.

Crystal Properties
Matthews coefficient	Solvent content
4.22	70.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 166.672	α = 90
b = 166.672	β = 90
c = 331.697	γ = 120

Symmetry
Space Group	P 65 2 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		2018-01-31	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.1	0.9141	BESSY	14.1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Rrim I (All)	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	3.6	50	98.9	0.748	0.993	4.86	13.1		32081			122.8

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3.6	3.81	96.4		8.886	0.123	0.35

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	3.7	48.924	29634	1482	99.2	0.269	0.2655	0.27	0.3328	0.33	172.198

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]
1.194	0.597		1.194		-3.873

RMS Deviations
Key	Refinement Restraint Deviation
r_lrange_it	36.36
r_scangle_it	25.467
r_mcangle_it	22.766
r_dihedral_angle_1_deg	20.224
r_dihedral_angle_3_deg	17.127
r_scbond_it	15.775
r_dihedral_angle_6_deg	15.735
r_mcbond_it	14.012
r_dihedral_angle_2_deg	5.901
r_paralell_plane_angle_deg	4.846
r_angle_refined_deg	1.211
r_symmetry_nbd_refined	0.421
r_nbtor_refined	0.315
r_nbd_refined	0.253
r_symmetry_xyhbond_nbd_refined	0.229
r_chiral_restr	0.203
r_xyhbond_nbd_refined	0.188
r_ext_dist_refined_b	0.04
r_gen_planes_refined	0.015
r_bond_refined_d	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9792
Nucleic Acid Atoms	1464
Solvent Atoms	8
Heterogen Atoms

Software

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