8PF2 | pdb_00008pf2

Structure of the Histidine Kinase CheA ATP-Binding domain in complex with compound ODDHK16

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	35.63

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 40.966	α = 90
b = 59.12	β = 97.277
c = 67.064	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	2.1	66.524	98.8	0.129	0.154	0.083	0.994	9.2	6.7		18456

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	2.1	2.16			1.205	1.451	0.796	0.682		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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.1	66.524	18443	946	98.605	0.188	0.185	0.2	0.2455	0.26	40.373

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]
-1.347		-1.54	0.805		0.906

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_other_2_deg	19.276
r_dihedral_angle_3_deg	16.809
r_dihedral_angle_2_deg	16.638
r_dihedral_angle_6_deg	15.848
r_lrange_other	12.839
r_lrange_it	12.833
r_scangle_it	10.867
r_scangle_other	10.864
r_scbond_it	7.449
r_scbond_other	7.447
r_dihedral_angle_1_deg	6.815
r_mcangle_it	5.276
r_mcangle_other	5.275
r_mcbond_it	4.145
r_mcbond_other	4.14
r_angle_refined_deg	2.169
r_angle_other_deg	0.831
r_symmetry_nbd_refined	0.371
r_symmetry_xyhbond_nbd_refined	0.365
r_nbd_other	0.275
r_xyhbond_nbd_other	0.265
r_nbd_refined	0.222
r_symmetry_nbd_other	0.175
r_nbtor_refined	0.169
r_ncsr_local_group_1	0.164
r_xyhbond_nbd_refined	0.144
r_chiral_restr	0.112
r_symmetry_nbtor_other	0.08
r_bond_refined_d	0.015
r_gen_planes_refined	0.013
r_bond_other_d	0.004
r_gen_planes_other	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2680
Nucleic Acid Atoms
Solvent Atoms	28
Heterogen Atoms	16

Software

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