6VBF | pdb_00006vbf

1.85 Angstrom Resolution Crystal Structure of N-terminal Domain of Two-component System Response Regulator from Acinetobacter baumannii

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	292	Protein: 7.6 mg/ml, 0.01M Tris pH 8.3; Screen: PEGs II (H8), 0.2M Calcium acetate, 0.1M HEPES pH 7.5, 10% (w/v) PEG 8000. Cryo: 0.2M Calcium chloride, 0.1M HEPES pH 7.5, 30 %(w/v) PEG 4000.

Crystal Properties
Matthews coefficient	Solvent content
2.68	54.1

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 51.819	α = 90
b = 51.819	β = 90
c = 194.504	γ = 120

Symmetry
Space Group	P 65

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	MARMOSAIC 300 mm CCD	C(111)	2019-11-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-G	0.97856	APS	21-ID-G

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (Observed)	Rrim I (All)	Rpim I (All)	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	1.85	30	99.9	0.071	0.071	0.077	0.029	28.2	6.9		25198		-3	29.2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.85	1.88	100		0.776	0.776	0.839	0.318	0.905	2.8	6.9

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	SAD	FREE R-VALUE	1.85	29.394	25072	1255	99.952	0.18	0.1778	0.1918	0.2161	0.2248	35.519

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]
0.662	0.331		0.662		-2.146

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	27.862
r_dihedral_angle_4_deg	11.526
r_dihedral_angle_3_deg	9.719
r_lrange_it	5.76
r_lrange_other	5.666
r_scangle_it	3.56
r_scangle_other	3.559
r_dihedral_angle_1_deg	3.546
r_mcangle_it	2.758
r_mcangle_other	2.758
r_scbond_it	2.458
r_scbond_other	2.457
r_mcbond_it	2.027
r_mcbond_other	1.926
r_angle_refined_deg	1.424
r_angle_other_deg	0.38
r_symmetry_xyhbond_nbd_refined	0.286
r_nbd_other	0.214
r_nbd_refined	0.212
r_symmetry_nbd_other	0.182
r_nbtor_refined	0.156
r_xyhbond_nbd_refined	0.138
r_symmetry_nbd_refined	0.121
r_symmetry_nbtor_other	0.087
r_chiral_restr	0.064
r_gen_planes_refined	0.053
r_gen_planes_other	0.049
r_bond_refined_d	0.005
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1908
Nucleic Acid Atoms
Solvent Atoms	141
Heterogen Atoms	5

Software

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