8QA9 | pdb_00008qa9

Crystal structure of the RK2 plasmid encoded co-complex of the C-terminally truncated transcriptional repressor protein KorB complexed with the partner repressor protein KorA bound to OA-DNA

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	8QA8
experimental model	PDB	2W7N

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6	293	NULL

Crystal Properties
Matthews coefficient	Solvent content
3.12	61

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 173.253	α = 90
b = 77.095	β = 107.42
c = 84.609	γ = 90

Symmetry
Space Group	C 1 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 EIGER2 XE 16M		2022-07-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.9763	Diamond	I03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	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	2.7	82.65	100	0.13	0.135	0.039	0.993	14.1	12.4		29438			58.1

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.7	2.83		100	1.533	1.606	0.473	0.677		11.6

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2.7	82.65	27994	1444	100	0.19402	0.191	0.2	0.25239	0.26	RANDOM	76.613

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]
-1.59		-0.6	2.24		-0.23

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	18.486
r_dihedral_angle_2_deg	10.653
r_long_range_B_refined	8.425
r_long_range_B_other	8.424
r_scangle_other	6.413
r_dihedral_angle_1_deg	6.216
r_mcangle_it	5.006
r_mcangle_other	5.005
r_scbond_it	4.398
r_scbond_other	4.168
r_mcbond_it	3.247
r_mcbond_other	3.23
r_angle_refined_deg	1.774
r_angle_other_deg	0.52
r_chiral_restr	0.077
r_bond_refined_d	0.008
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_dihedral_angle_4_deg
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
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4942
Nucleic Acid Atoms	568
Solvent Atoms	19
Heterogen Atoms	25

Software

Software
Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
DIALS	data reduction
PHASER	phasing