3D40

Crystal structure of fosfomycin resistance kinase FomA from Streptomyces wedmorensis complexed with diphosphate

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	295	11% PEG 3350, 0.1 M tri-ammonium citrate, 0.1 M MES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.88	57.37

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 88.361	α = 90
b = 88.361	β = 90
c = 79.046	γ = 120

Symmetry
Space Group	P 32 2 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	CCD	MAR CCD 165 mm	mirrors	2007-03-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CAMD BEAMLINE GCPCC	1.38079	CAMD	GCPCC

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym I (Observed)	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	1.53	30	97.9	0.04	34.8	5.2	52986	52986		-3	27.7

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.53	1.58	85.3		0.51	2.9	4.6	4585

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	model of SeMet FomA form based on MAD data	1.53	27.49	50201	50201	834	94.29	0.16908	0.16908	0.16864	0.19801	RANDOM	26.933

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]
0.36	0.18		0.36		-0.54

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.6
r_dihedral_angle_4_deg	14.671
r_dihedral_angle_3_deg	13.526
r_dihedral_angle_1_deg	5.409
r_scangle_it	4.418
r_scbond_it	2.803
r_mcangle_it	1.917
r_angle_refined_deg	1.738
r_mcbond_it	1.25
r_nbtor_refined	0.318

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.6
r_dihedral_angle_4_deg	14.671
r_dihedral_angle_3_deg	13.526
r_dihedral_angle_1_deg	5.409
r_scangle_it	4.418
r_scbond_it	2.803
r_mcangle_it	1.917
r_angle_refined_deg	1.738
r_mcbond_it	1.25
r_nbtor_refined	0.318
r_nbd_refined	0.211
r_symmetry_hbond_refined	0.175
r_symmetry_vdw_refined	0.169
r_xyhbond_nbd_refined	0.158
r_chiral_restr	0.123
r_bond_refined_d	0.016
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1953
Nucleic Acid Atoms
Solvent Atoms	231
Heterogen Atoms	9

Software

Software
Software Name	Purpose
REFMAC	refinement
MAR345dtb	data collection
HKL-2000	data reduction
HKL-2000	data scaling
AMoRE	phasing

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.