7S6E

Crystal structure of UrtA from Synechococcus CC9311 in complex with urea and calcium

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		295	0.062 M MES; 0.038 imidazole, pH 6.5, 0.03M MgCl2, 0.03M CaCl2.2H2O, 12.5% w/v PEG 1000, 12.5% w/v PEG 3350, 12.5% v/v MPD

Crystal Properties
Matthews coefficient	Solvent content
2.01	38.95

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 49.76	α = 90
b = 117.12	β = 90
c = 123.46	γ = 90

Symmetry
Space Group	P 21 21 21

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		2020-06-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I23	3.0240, 3.3509, 4.2753, 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	1.97	85.114	93.3	0.076	0.08	0.026	0.999	22.8	15.6		49942

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	1.97	2.02			0.295	0.343	0.172	0.945		6.7

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	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	SAD	FREE R-VALUE	1.973	85.114	49942	2526	96.577	0.148	0.1467	0.1737	22.602

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]
0.669			0.378		-1.047

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.869
r_dihedral_angle_4_deg	18.648
r_dihedral_angle_3_deg	12.858
r_dihedral_angle_1_deg	6.739
r_lrange_it	5.03
r_lrange_other	5.025
r_scangle_it	4.077
r_scangle_other	4.077
r_scbond_it	2.796
r_scbond_other	2.795
r_mcangle_it	2.365
r_mcangle_other	2.365
r_mcbond_it	1.862
r_mcbond_other	1.857
r_angle_refined_deg	1.64
r_angle_other_deg	1.415
r_nbd_other	0.274
r_nbd_refined	0.207
r_symmetry_nbd_refined	0.202
r_symmetry_xyhbond_nbd_refined	0.182
r_symmetry_nbd_other	0.179
r_nbtor_refined	0.172
r_metal_ion_refined	0.163
r_xyhbond_nbd_refined	0.153
r_symmetry_metal_ion_refined	0.134
r_chiral_restr	0.09
r_symmetry_nbtor_other	0.081
r_bond_refined_d	0.012
r_gen_planes_refined	0.01
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6217
Nucleic Acid Atoms
Solvent Atoms	637
Heterogen Atoms	61

Software

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