2O3O | pdb_00002o3o

Crystal Structure of the sensor histidine kinase regulator YycI from Bacillus subtitlis

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		3.2	293	18% PEG1500, 100 MM CITRATE BUFFER, 200 mM lithium sulfate, pH 3.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K, pH 3.20

Crystal Properties
Matthews coefficient	Solvent content
2.5	50.72

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 60.792	α = 90
b = 161.922	β = 90.9
c = 180.156	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	CCD			2006-05-20	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 12.3.1	0.94645, 0.97969, 0.97955	ALS	12.3.1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	2.89	90	92.7	0.084	12.4	3.8		71733		-4

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.89	2.97	53.9		0.334	1.4	2.1

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	MAD	THROUGHOUT	2.89	90	68065	3605	92.2	0.214	0.212	0.25	0.262	0.29	RANDOM	25.71

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]
-0.35		0.23	-1.22		1.58

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.071
r_dihedral_angle_4_deg	17.812
r_dihedral_angle_3_deg	17.733
r_dihedral_angle_1_deg	6.655
r_scangle_it	6.394
r_scbond_it	4.636
r_mcangle_it	2.796
r_mcbond_it	1.925
r_angle_refined_deg	1.169
r_angle_other_deg	0.764
r_mcbond_other	0.386
r_nbd_refined	0.206
r_nbtor_refined	0.184
r_nbd_other	0.18
r_symmetry_vdw_other	0.177
r_symmetry_vdw_refined	0.165
r_xyhbond_nbd_refined	0.148
r_symmetry_hbond_refined	0.089
r_nbtor_other	0.085
r_chiral_restr	0.069
r_bond_refined_d	0.01
r_xyhbond_nbd_other	0.004
r_gen_planes_refined	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	23395
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	6

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
SHELXD	phasing
SHARP	phasing