5O3S | pdb_00005o3s

Carbon regulatory PII-like protein SbtB from Synechocystis sp. 6803 in Apo state, hexagonal crystal form

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5O3P

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	8.5	293.15	Protein solution containing 19 mg/ml SbtB in 50 mM Tris.HCl (pH 8.0), 250 mM NaCl mixed 1:1 with reservoir solution composed of 0.2 M Mg chloride, 0.1 M Tris.HCl pH 8.5, and 30% (w/v) PEG 4000.

Crystal Properties
Matthews coefficient	Solvent content
1.77	30.69

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 50.535	α = 90
b = 50.535	β = 90
c = 64.951	γ = 120

Symmetry
Space Group	P 63

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-F		2015-11-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	1	SLS	X10SA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	2.2	36.29	100	0.095	0.996	12.25	10.1		4838

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.2	2.33	100		0.764	0.934	2.12	9.8

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	MOLECULAR REPLACEMENT	THROUGHOUT	5O3P	2.2	36.29	4256	581	99.94	0.23109	0.2261	0.24	0.26763	0.27	RANDOM	68.915

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]
-3.45	-1.73		-3.45		11.21

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.556
r_dihedral_angle_3_deg	11.089
r_dihedral_angle_4_deg	8.514
r_dihedral_angle_1_deg	3.93
r_long_range_B_refined	1.441
r_long_range_B_other	1.441
r_angle_refined_deg	0.741
r_mcangle_it	0.736
r_mcangle_other	0.736
r_angle_other_deg	0.635
r_scangle_other	0.599
r_mcbond_it	0.407
r_mcbond_other	0.407
r_scbond_it	0.36
r_scbond_other	0.36
r_chiral_restr	0.045
r_bond_refined_d	0.004
r_gen_planes_refined	0.002
r_bond_other_d	0.001
r_gen_planes_other	0.001
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	711
Nucleic Acid Atoms
Solvent Atoms	7
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
MOLREP	phasing