8H7E | pdb_00008h7e

Crystal structure of a de novo enzyme, ferric enterobactin esterase Syn-F4 (K4T) at 2.0 angstrom resolution

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	8H7C

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.9	293	0.1M Tris, 0.2M ammonium acetate, 15% PEG 3350 (After crystallization, ferric enterobactin was added.)

Crystal Properties
Matthews coefficient	Solvent content
1.98	37.73

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 47.342	α = 90
b = 61.391	β = 90
c = 135.729	γ = 90

Symmetry
Space Group	C 2 2 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	95	PIXEL	DECTRIS PILATUS3 S 6M	Focusing Mirror	2019-02-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE BL-5A	1.000	Photon Factory	BL-5A

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	2	50	88.3	0.104	0.109	0.031	5.4	11.6		12201

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	2	2.03	59.9		0.664	0.701	0.218	0.839		9.6

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	8H7C	2	50	9988	538	76.38	0.21967	0.21714	0.22	0.26624	0.27	RANDOM	35.875

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]
-0.05			-0.45		0.5

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.735
r_dihedral_angle_3_deg	16.696
r_dihedral_angle_4_deg	16.636
r_long_range_B_refined	6.553
r_long_range_B_other	6.544
r_dihedral_angle_1_deg	4.724
r_scangle_other	4.255
r_angle_other_deg	3.523
r_mcangle_other	3.209
r_mcangle_it	3.204
r_scbond_it	2.514
r_scbond_other	2.513
r_mcbond_it	1.983
r_mcbond_other	1.968
r_angle_refined_deg	1.235
r_chiral_restr	0.074
r_bond_refined_d	0.01
r_gen_planes_other	0.009
r_gen_planes_refined	0.005
r_bond_other_d
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	1567
Nucleic Acid Atoms
Solvent Atoms	75
Heterogen Atoms	4

Software

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