8E7R

Crystal Structure of FosB from Bacillus cereus with Zinc and Phosphonoacetate

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 phosphonoacetate

Crystal Properties
Matthews coefficient	Solvent content
2.32	46.97

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 64.674	α = 90
b = 67.831	β = 90
c = 69.738	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	1.975	50	99.8	0.16	0.178	0.077	3.6	5.2		22012

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	1.98	2.01	99.8		0.583	0.652	0.287	0.752		5

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	1.975	46.808	21965	1049	99.223	0.172	0.1691	0.2204	RANDOM	17.79

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]
0.01			-0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.881
r_dihedral_angle_3_deg	13.531
r_dihedral_angle_2_deg	7.656
r_dihedral_angle_1_deg	6.97
r_lrange_it	4.779
r_lrange_other	4.673
r_scangle_it	3.113
r_scangle_other	3.113
r_scbond_it	1.97
r_scbond_other	1.956
r_mcangle_it	1.928
r_mcangle_other	1.927
r_angle_refined_deg	1.444
r_mcbond_it	1.296
r_mcbond_other	1.295
r_angle_other_deg	0.779
r_nbd_refined	0.22
r_symmetry_nbd_other	0.21
r_nbd_other	0.196
r_nbtor_refined	0.181
r_xyhbond_nbd_refined	0.155
r_symmetry_nbd_refined	0.149
r_symmetry_xyhbond_nbd_refined	0.131
r_symmetry_nbtor_other	0.084
r_metal_ion_refined	0.079
r_chiral_restr	0.073
r_gen_planes_other	0.01
r_gen_planes_refined	0.008
r_bond_refined_d	0.007
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2326
Nucleic Acid Atoms
Solvent Atoms	211
Heterogen Atoms	35

Software

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