8PNO

The MgF3(H2O) transition state analog complex of E. coli YihX

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2B0C

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		277	20 mg/mL YihX in Tris-HCl 25 mM pH 7.5, NaCl 150 mM, MgCl2 20 mM, NaF 30 mM was mixed 1:1 ratio with precipitant containing MES 55.5 mM, imidazole 44.5 mM pH 6.5, 20% PEG500, 30 mM MgCl2, 30 mM CaCl2, 20% glycerol, 10% PEG4000. The crystals are further soaked with the precipitant supplemented with 50 mM MgCl2 and 100 mM NH4F

Crystal Properties
Matthews coefficient	Solvent content
4.43	71.97

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 67.259	α = 90
b = 79.325	β = 108.52
c = 80.297	γ = 90

Symmetry
Space Group	P 1 21 1

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	DECTRIS EIGER2 XE 16M		2022-04-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.9762	Diamond	I03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.2	58.97	100	0.992	5.8	6.9		40811

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	2.2	2.27			0.664	1

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2.2	59.04	38765	2023	99.92	0.21376	0.21152	0.25711	RANDOM	38.806

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]
-0.33		-0.56	-3.87		3.74

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	15.471
r_dihedral_angle_2_deg	8.552
r_long_range_B_refined	7.69
r_long_range_B_other	7.689
r_dihedral_angle_1_deg	7.156
r_scangle_other	5.431
r_mcangle_it	4.802
r_mcangle_other	4.801
r_scbond_it	3.721
r_scbond_other	3.721
r_mcbond_it	3.183
r_mcbond_other	3.182
r_angle_refined_deg	1.481
r_angle_other_deg	0.489
r_chiral_restr	0.065
r_bond_refined_d	0.008
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_dihedral_angle_4_deg
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3196
Nucleic Acid Atoms
Solvent Atoms	231
Heterogen Atoms	111

Software

Software
Software Name	Purpose
REFMAC	refinement
xia2	data reduction
Aimless	data scaling
MOLREP	phasing