7NE9 | pdb_00007ne9

A single sensor controls large variations in zinc quotas in a marine cyanobacterium

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	6	277	100 mM magnesium acetate, 100 mM MES pH 6, 16% (w/v) PEG 10000

Crystal Properties
Matthews coefficient	Solvent content
3.14	60.78

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 129.25	α = 90
b = 129.25	β = 90
c = 77.28	γ = 120

Symmetry
Space Group	P 65

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	PSI PILATUS 6M		2017-10-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	1.2827	Diamond	I03

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	2.1	77.3	99.9	0.193	0.999	19.4	39.8		43002

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.1	2.21	99.6		0.754

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	THROUGHOUT	2.1	64.625	43002	1654	99.998	0.195	0.1944	0.21	0.2178	0.23	47.106

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]
0.359	0.179		0.359		-1.164

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.608
r_dihedral_angle_other_3_deg	26.697
r_dihedral_angle_4_deg	22.274
r_dihedral_angle_3_deg	13.19
r_lrange_it	6.779
r_lrange_other	6.777
r_dihedral_angle_1_deg	6.521
r_scangle_it	4.377
r_scangle_other	4.377
r_mcangle_it	3.681
r_mcangle_other	3.681
r_scbond_it	3.069
r_scbond_other	3.069
r_mcbond_it	2.184
r_mcbond_other	2.167
r_angle_refined_deg	1.608
r_angle_other_deg	1.373
r_symmetry_nbd_refined	0.212
r_symmetry_xyhbond_nbd_refined	0.205
r_nbd_refined	0.204
r_symmetry_nbd_other	0.191
r_xyhbond_nbd_refined	0.179
r_nbd_other	0.166
r_nbtor_refined	0.154
r_ncsr_local_group_6	0.133
r_ncsr_local_group_3	0.131
r_ncsr_local_group_1	0.125
r_ncsr_local_group_4	0.125
r_ncsr_local_group_2	0.119
r_symmetry_nbtor_other	0.109
r_ncsr_local_group_5	0.101
r_chiral_restr	0.071
r_bond_refined_d	0.014
r_gen_planes_refined	0.007
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3712
Nucleic Acid Atoms
Solvent Atoms	140
Heterogen Atoms	13

Software

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