7OYK | pdb_00007oyk

DNA-binding domain of CggR in complex with the DNA operator

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	290	10% (w/v) PEG 3350, 100mM MES, pH 6.5, 100mM calcium chloride, 13% (v/v) glycerol

Crystal Properties
Matthews coefficient	Solvent content
2.07	40.53

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 57.972	α = 90
b = 103.141	β = 90.537
c = 51.111	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 PILATUS 6M		2020-06-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.2	0.9797	BESSY	14.2

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	2.1	50	96.8	0.086	0.998	9.4	2.3		34417			46.7

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	2.1	2.23	95.4		1.111	0.514	1.1	2.3

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	SAD	THROUGHOUT	2.101	45.837	32691	1726	98.169	0.21	0.208	0.2192	0.2527	0.2615	43.543

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]
-0.001		-0.007	-0.002		0.003

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.54
r_dihedral_angle_4_deg	20.05
r_dihedral_angle_3_deg	15.226
r_lrange_it	8.281
r_lrange_other	8.28
r_scangle_it	6.351
r_scangle_other	6.35
r_dihedral_angle_1_deg	5.35
r_mcangle_it	4.705
r_mcangle_other	4.704
r_scbond_it	4.234
r_scbond_other	4.233
r_mcbond_it	3.314
r_mcbond_other	3.314
r_angle_other_deg	2.192
r_angle_refined_deg	1.336
r_nbd_other	0.356
r_symmetry_xyhbond_nbd_refined	0.233
r_symmetry_nbd_other	0.229
r_symmetry_nbd_refined	0.21
r_nbd_refined	0.209
r_xyhbond_nbd_refined	0.181
r_nbtor_refined	0.171
r_metal_ion_refined	0.158
r_symmetry_nbtor_other	0.069
r_chiral_restr	0.068
r_bond_other_d	0.028
r_symmetry_xyhbond_nbd_other	0.012
r_gen_planes_other	0.009
r_gen_planes_refined	0.008
r_bond_refined_d	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3045
Nucleic Acid Atoms	1950
Solvent Atoms	139
Heterogen Atoms	16

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
SHELXDE	phasing