7S6F | pdb_00007s6f

Crystal structure of UrtA1 from Synechococcus WH8102 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	7.5	295	0.05 M Sodium Hepes: MOPS pH 7.5, 0.03 MgCl2, 0.03 CaCl2; 20 % PEG 500 MME; 10 % Peg 20000 Cryo: 30 % Ethylene Glycol

Crystal Properties
Matthews coefficient	Solvent content
2.29	46.53

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 47.51	α = 90
b = 71.39	β = 90
c = 120.46	γ = 90

Symmetry
Space Group	P 21 2 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		2020-02-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I23	2.7552	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	1.8	120.46	91.3	0.156	0.16	0.032	0.999	18	38.4		35399

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	1.8	1.84	76		2.902	3.139	1.122	0.161		12.5

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	1.8	71.492	35358	1775	91.131	0.161	0.159	0.17	0.1903	0.19	33.343

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]
0.777			0.797		-1.574

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.76
r_dihedral_angle_3_deg	14.113
r_dihedral_angle_4_deg	10.763
r_dihedral_angle_1_deg	6.913
r_lrange_it	5.897
r_lrange_other	5.862
r_scangle_it	5.09
r_scangle_other	5.089
r_scbond_it	3.531
r_scbond_other	3.53
r_mcangle_it	2.854
r_mcangle_other	2.854
r_mcbond_it	2.299
r_mcbond_other	2.298
r_angle_refined_deg	1.612
r_angle_other_deg	1.409
r_symmetry_xyhbond_nbd_refined	0.228
r_nbd_refined	0.2
r_symmetry_nbd_other	0.173
r_nbtor_refined	0.171
r_nbd_other	0.158
r_xyhbond_nbd_refined	0.134
r_symmetry_nbd_refined	0.127
r_metal_ion_refined	0.106
r_chiral_restr	0.085
r_symmetry_nbtor_other	0.081
r_symmetry_xyhbond_nbd_other	0.015
r_symmetry_metal_ion_refined	0.012
r_bond_refined_d	0.01
r_gen_planes_refined	0.009
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3064
Nucleic Acid Atoms
Solvent Atoms	263
Heterogen Atoms	17

Software

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