8P3R

Structure of the Histidine Kinase CheA ATP-Binding domain in complex with compound ODDHK4

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1I58

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5	294.15	PEG 8000 30% Ammonium acetate 0.6 M Sodium acetate 0.065 M ph 4.5

Crystal Properties
Matthews coefficient	Solvent content
1.91	35.62

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 41.088	α = 90
b = 59.182	β = 97.118
c = 66.766	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		2019-04-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALBA BEAMLINE XALOC	0.979510	ALBA	XALOC

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	1.9	66.251	99.3	0.071	0.084	0.045	0.998	15.1	6.6		24981

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	1.9	1.949			0.384	0.457	0.245	0.957		6.7

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	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.9	66.251	24966	1159	99.138	0.183	0.1804	0.2285	32.304

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]
-1.674		0.097	0.434		1.179

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	16.663
r_dihedral_angle_6_deg	16.289
r_dihedral_angle_2_deg	11.887
r_lrange_it	11.704
r_lrange_other	11.704
r_scangle_it	10.677
r_scangle_other	10.674
r_scbond_it	7.439
r_scbond_other	7.439
r_dihedral_angle_1_deg	5.867
r_mcangle_it	5.375
r_mcangle_other	5.373
r_mcbond_it	4.17
r_mcbond_other	4.146
r_angle_refined_deg	2.045
r_angle_other_deg	0.671
r_symmetry_nbd_refined	0.327
r_symmetry_xyhbond_nbd_refined	0.309
r_nbd_other	0.283
r_nbd_refined	0.237
r_symmetry_nbd_other	0.193
r_nbtor_refined	0.18
r_xyhbond_nbd_refined	0.138
r_ncsr_local_group_1	0.123
r_chiral_restr	0.102
r_symmetry_nbtor_other	0.087
r_bond_refined_d	0.015
r_gen_planes_refined	0.012
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2689
Nucleic Acid Atoms
Solvent Atoms	59
Heterogen Atoms	18

Software

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