7Y9I

Complex structure of AtYchF1 with ppGpp

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5EE0

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.6	277	PEG

Crystal Properties
Matthews coefficient	Solvent content
2.55	51.83

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 72.46	α = 90
b = 111.5	β = 90
c = 52.33	γ = 90

Symmetry
Space Group	P 21 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	113	PIXEL	DECTRIS PILATUS 2M		2019-03-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL17B1	0.9792	SSRF	BL17B1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	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	2.07	50.01	99.9	0.073	0.028	18.8	13		26569

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rpim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.07	2.12			0.392

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 (All)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	NONE	5EE0	2.07	50.005	26522	1367	99.853	0.207	0.2056	0.2355	48.867

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]
-2.63			-0.066		2.696

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.32
r_dihedral_angle_4_deg	18.727
r_dihedral_angle_3_deg	13.223
r_lrange_it	6.851
r_lrange_other	6.828
r_dihedral_angle_1_deg	6.521
r_scangle_it	5.618
r_scangle_other	5.618
r_mcangle_it	4.339
r_mcangle_other	4.338
r_scbond_it	3.675
r_scbond_other	3.673
r_mcbond_it	3.08
r_mcbond_other	3.08
r_angle_refined_deg	1.425
r_angle_other_deg	1.253
r_nbd_refined	0.189
r_nbd_other	0.177
r_symmetry_nbd_other	0.165
r_nbtor_refined	0.158
r_symmetry_nbd_refined	0.15
r_xyhbond_nbd_refined	0.148
r_symmetry_xyhbond_nbd_refined	0.122
r_symmetry_nbtor_other	0.076
r_chiral_restr	0.059
r_bond_refined_d	0.006
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2785
Nucleic Acid Atoms
Solvent Atoms	61
Heterogen Atoms	37

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing