8E7Q

Crystal Structure of FosB from Bacillus cereus with Zinc and 2-Phosphonopropionic acid

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4JH6

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	298	16% PEG 3350, 125 mM magnesium formate, 5 mM 2-phosphonopropionic acid

Crystal Properties
Matthews coefficient	Solvent content
2.32	46.97

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 64.314	α = 90
b = 68.016	β = 90
c = 69.802	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	100	PIXEL	DECTRIS EIGER X 16M		2022-06-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID	1.0	APS	22-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	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	1.9	50	97.6	0.141	0.158	0.069	3.7	5		24190

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	1.9	1.93	98.3		0.57	0.634	0.274	0.775		5.1

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	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	4JH6	1.9	38.832	24142	1092	97.524	0.171	0.1693	0.2188	RANDOM	17.204

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]
0.005			-0.004		-0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	17.699
r_dihedral_angle_3_deg	13.193
r_dihedral_angle_1_deg	6.845
r_dihedral_angle_2_deg	6.136
r_lrange_it	5.389
r_lrange_other	5.291
r_scangle_it	3.49
r_scangle_other	3.489
r_mcangle_it	2.568
r_mcangle_other	2.567
r_scbond_it	2.213
r_scbond_other	2.212
r_mcbond_it	1.732
r_mcbond_other	1.72
r_angle_refined_deg	1.489
r_angle_other_deg	0.805
r_nbd_refined	0.229
r_symmetry_nbd_refined	0.229
r_nbd_other	0.219
r_symmetry_nbd_other	0.209
r_nbtor_refined	0.181
r_xyhbond_nbd_refined	0.155
r_symmetry_xyhbond_nbd_refined	0.154
r_symmetry_nbtor_other	0.085
r_chiral_restr	0.077
r_symmetry_xyhbond_nbd_other	0.076
r_metal_ion_refined	0.076
r_gen_planes_other	0.011
r_bond_refined_d	0.008
r_gen_planes_refined	0.008
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2326
Nucleic Acid Atoms
Solvent Atoms	218
Heterogen Atoms	25

Software

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