8SUA | pdb_00008sua

Structure of M. baixiangningiae DarR-ligand complex

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		273	1.5 M NaCl, 0.2 M MgCl2, 0.1 M Tris

Crystal Properties
Matthews coefficient	Solvent content
2.8	56.09

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 85.437	α = 90
b = 85.437	β = 90
c = 62.436	γ = 120

Symmetry
Space Group	P 32 2 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		2022-02-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 5.0.2	1.0	ALS	5.0.2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym I (Observed)	Rpim 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	1.6	47.72	99.9	0.047	0.02	1	25.2	11.2		35029

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.6	1.64			0.503	0.406	0.805	2.1

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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)	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	1.6	47.72	1.34	35029	1775	99.93	0.1853	0.1841	0.1876	0.209	0.2078

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]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	4.126
f_angle_d	1.15
f_chiral_restr	0.055
f_bond_d	0.013
f_plane_restr	0.012

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1509
Nucleic Acid Atoms
Solvent Atoms	186
Heterogen Atoms	15

Software

Software
Software Name	Purpose
PHENIX	refinement
SCALA	data scaling
XDS	data reduction
AutoSol	phasing