2P7K | pdb_00002p7k

Crystal structure of genomically encoded fosfomycin resistance protein, FosX, from Listeria monocytogenes (hexagonal form)

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1R9C	PDB ENTRY 1R9C

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.6	295	15% PEG 8000, 20 mM Na acetate, 0.1 M Na citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
3.7	66.71

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 83.524	α = 90
b = 83.524	β = 90
c = 114.446	γ = 120

Symmetry
Space Group	P 61

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	2002-01-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CAMD BEAMLINE GCPCC	1.069	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	3.3	30	99.4	0.099	6.83	4.5	6831	6831		-3

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	3.3	3.42	99.9		0.44	1.3	4.9	666

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 (Depositor)	R-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1R9C	3.3	15	5815	5815	293	90.19	0.23	0.23	0.228	0.277	RANDOM

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]
2.51	1.26		2.51		-3.77

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.279
r_dihedral_angle_4_deg	22.27
r_dihedral_angle_3_deg	20.328
r_dihedral_angle_1_deg	6.819
r_angle_refined_deg	1.244
r_scangle_it	1.183
r_scbond_it	0.684
r_mcangle_it	0.51
r_nbtor_refined	0.327
r_mcbond_it	0.272

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.279
r_dihedral_angle_4_deg	22.27
r_dihedral_angle_3_deg	20.328
r_dihedral_angle_1_deg	6.819
r_angle_refined_deg	1.244
r_scangle_it	1.183
r_scbond_it	0.684
r_mcangle_it	0.51
r_nbtor_refined	0.327
r_mcbond_it	0.272
r_nbd_refined	0.236
r_symmetry_vdw_refined	0.199
r_xyhbond_nbd_refined	0.135
r_chiral_restr	0.073
r_bond_refined_d	0.011
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1904
Nucleic Acid Atoms
Solvent Atoms	6
Heterogen Atoms	26

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 U.S. National Science Foundation (DBI-2321666), 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 R01GM157729.