8G7H | pdb_00008g7h

Crystal Structure of FosB from Bacillus cereus with Zinc and (1-hydroxypropan-2-yl)phosphonic 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		298	Protein solution (10 mg/mL FosB in 20 mM HEPES buffer, pH 7.5 and 5 mM inhibitor) and reservoir solution (75 mM Mg formate and 14% (w/v) PEG 3350) were mixed in a Hampton Research VDX plate using a 2:3 ratio of protein:reservoir solutions. Cryoprotected in its reservoir solution with 20% glycerol added prior to rapid freezing in liquid nitrogen

Crystal Properties
Matthews coefficient	Solvent content
2.29	46.24

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 64.233	α = 90
b = 68.21	β = 90
c = 69.826	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		2022-09-26	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)	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	1.81	50	99.9	0.138	0.145	0.044	0.994	4.1	10.7		28683

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	1.81	1.84	100		0.785	0.829	0.263	0.841		9.5

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	4JH6	1.81	48.793	28626	1462	99.725	0.156	0.1543	0.17	0.1852	0.2	RANDOM	19.454

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]
0.002			-0.004		0.002

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	17.519
r_dihedral_angle_3_deg	13.282
r_dihedral_angle_1_deg	6.897
r_lrange_it	6.454
r_lrange_other	6.342
r_dihedral_angle_2_deg	5.582
r_scangle_it	4.495
r_scangle_other	4.493
r_scbond_it	2.835
r_scbond_other	2.834
r_mcangle_it	2.187
r_mcangle_other	2.187
r_mcbond_it	1.603
r_mcbond_other	1.602
r_angle_refined_deg	1.52
r_angle_other_deg	0.832
r_nbd_refined	0.231
r_symmetry_nbd_refined	0.212
r_symmetry_nbd_other	0.21
r_nbd_other	0.207
r_nbtor_refined	0.193
r_symmetry_xyhbond_nbd_other	0.19
r_xyhbond_nbd_refined	0.163
r_symmetry_xyhbond_nbd_refined	0.158
r_metal_ion_refined	0.115
r_symmetry_nbtor_other	0.084
r_chiral_restr	0.079
r_gen_planes_other	0.012
r_gen_planes_refined	0.009
r_bond_refined_d	0.008
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2324
Nucleic Acid Atoms
Solvent Atoms	270
Heterogen Atoms	47

Software

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