9P6I | pdb_00009p6i

Crystal Structure of the Histidine Kinase VC2136 from Vibrio cholerae serotype O1

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	292	Protein: 6.5 mg/ml, 0.15M Sodium chloride, 0.01M Tris pH 8.3; Screen: Anions (G8), 0.37M Sodium sulfate, 0.1M MES pH 6.5. Cryo: 2M Lithium sulfate.

Crystal Properties
Matthews coefficient	Solvent content
2.6	52.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 86.211	α = 90
b = 86.211	β = 90
c = 212.636	γ = 120

Symmetry
Space Group	P 31

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 EIGER X 9M		2021-09-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-D	0.97848	APS	21-ID-D

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2.75	30	99.9	0.106	0.106	0.034	0.995	23.9	10.7		45970		-3	68.8

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.75	2.8	100		0.418	0.634	1.9	10.9

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	SAD	THROUGHOUT	2.75	28.22	43575	2322	99.88	0.2425	0.24022	0.2591	0.28631	0.2999	RANDOM	93.051

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]
16.29			16.29		-32.58

RMS Deviations
Key	Refinement Restraint Deviation
r_long_range_B_refined	8.187
r_long_range_B_other	8.148
r_mcangle_it	3.944
r_mcangle_other	3.943
r_scangle_other	3.743
r_dihedral_angle_3_deg	2.793
r_mcbond_it	2.363
r_mcbond_other	2.362
r_scbond_it	2.316
r_scbond_other	2.209
r_dihedral_angle_2_deg	1.587
r_dihedral_angle_1_deg	0.853
r_angle_refined_deg	0.845
r_angle_other_deg	0.665
r_chiral_restr	0.041
r_gen_planes_refined	0.003
r_gen_planes_other	0.003
r_bond_refined_d	0.002
r_bond_other_d	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	10887
Nucleic Acid Atoms
Solvent Atoms	57
Heterogen Atoms	213

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHENIX	phasing