7UG8 | pdb_00007ug8

Crystal structure of a solute receptor from Synechococcus CC9311 in complex with alpha-ketovaleric and calcium

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	295	0.02 M Sodium/Potassium Phosphate, 0.1M Bis Tris propane 7.5, 20% Peg 3350 Cryo: 30 % Peg 400

Crystal Properties
Matthews coefficient	Solvent content
2.05	39.99

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 54.68	α = 69.649
b = 54.75	β = 77.732
c = 61.15	γ = 67.267

Symmetry
Space Group	P 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	50	PIXEL	DECTRIS PILATUS 12M		2019-12-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I23	2.7552, 3.1790, 3.4925, 4.7686	Diamond	I23

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	1.796	50.277	90.9	0.068	0.073	0.024	0.999	16.8	13.6		50762

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	9.06	50.23			0.039	0.041	0.012	0.999		23.3

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	1.796	50.277	50762	2454	89.014	0.17	0.1687	0.18	0.1898	0.2	44.394

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]
2.341	-1.224	-0.948	-1.642	1.715	-0.183

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.739
r_dihedral_angle_3_deg	15.109
r_dihedral_angle_4_deg	13.801
r_lrange_other	8.054
r_lrange_it	8.05
r_scangle_it	6.79
r_scangle_other	6.79
r_dihedral_angle_1_deg	6.345
r_mcangle_it	5.008
r_mcangle_other	5.008
r_scbond_it	4.753
r_scbond_other	4.748
r_mcbond_it	3.873
r_mcbond_other	3.867
r_angle_refined_deg	1.509
r_angle_other_deg	1.375
r_symmetry_xyhbond_nbd_refined	0.263
r_nbd_other	0.205
r_nbd_refined	0.201
r_symmetry_nbd_other	0.181
r_nbtor_refined	0.169
r_xyhbond_nbd_refined	0.152
r_symmetry_nbd_refined	0.129
r_symmetry_xyhbond_nbd_other	0.111
r_metal_ion_refined	0.108
r_ncsr_local_group_1	0.097
r_symmetry_nbtor_other	0.082
r_chiral_restr	0.081
r_bond_refined_d	0.009
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5159
Nucleic Acid Atoms
Solvent Atoms	255
Heterogen Atoms	26

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
CRANK2	phasing
Coot	model building