5NC4 | pdb_00005nc4

Crystal structure of the ferric enterobactin receptor (PfeA) in complex with protochelin from Pseudomonas aeruginosa

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5M9K

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	6.5	294	PEG 8000, ADA, Magnesium acetate

Crystal Properties
Matthews coefficient	Solvent content
3.39	63.66

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 86.751	α = 90
b = 157.352	β = 90
c = 78.108	γ = 90

Symmetry
Space Group	P 21 21 2

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 PILATUS3 6M		2016-04-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I24	0.9686	Diamond	I24

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	2.8	157.35	100	0.054	0.999	19.5	7.2		26955

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.8	2.813	97.6		0.695	0.867	2.3	7.7

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 (Observed)	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	5M9K	2.8	78.68	25602	1310	99.93	0.22026	0.21811	0.22	0.26326	0.25	RANDOM	110.265

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]
2.46			2.15		-4.61

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.952
r_dihedral_angle_3_deg	17.1
r_dihedral_angle_4_deg	16.549
r_long_range_B_refined	11.031
r_long_range_B_other	11.031
r_dihedral_angle_1_deg	9.506
r_scangle_other	8.398
r_mcangle_it	7.583
r_mcangle_other	7.536
r_scbond_it	6.095
r_scbond_other	6.094
r_mcbond_it	5.596
r_mcbond_other	5.571
r_angle_refined_deg	1.406
r_angle_other_deg	0.708
r_chiral_restr	0.097
r_gen_planes_refined	0.015
r_bond_refined_d	0.012
r_gen_planes_other	0.002
r_bond_other_d	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5363
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	46

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing