8H7C | pdb_00008h7c

Crystal structure of a de novo enzyme, ferric enterobactin esterase Syn-F4 (K4T) - Pt derivative

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.9	293	0.1M Tris, 0.2M ammonium acetate, 8% PEG 3350 (soaking in 10mM K2PtCl4 for 1 day)

Crystal Properties
Matthews coefficient	Solvent content
1.91	35.44

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 47.986	α = 90
b = 61.468	β = 90
c = 128.991	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	2018-11-18	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE BL-5A	1.073, 1.069, 1.045	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	2.15	50	95.5	0.075	0.078	0.022	5.5	11.7		10257

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	2.15	2.19	71.6		0.5	0.532	0.174	0.922		7.8

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	MAD	THROUGHOUT	2.15	50	8975	464	88.08	0.2347	0.2327	0.24	0.2704	0.27	RANDOM	35.834

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]
-0.02			-0.13		0.15

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.711
r_dihedral_angle_3_deg	18.186
r_dihedral_angle_4_deg	15.645
r_dihedral_angle_1_deg	5.206
r_angle_refined_deg	1.265
r_angle_other_deg	0.926
r_chiral_restr	0.072
r_bond_refined_d	0.009
r_bond_other_d	0.006
r_gen_planes_refined	0.004

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.711
r_dihedral_angle_3_deg	18.186
r_dihedral_angle_4_deg	15.645
r_dihedral_angle_1_deg	5.206
r_angle_refined_deg	1.265
r_angle_other_deg	0.926
r_chiral_restr	0.072
r_bond_refined_d	0.009
r_bond_other_d	0.006
r_gen_planes_refined	0.004
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1576
Nucleic Acid Atoms
Solvent Atoms	41
Heterogen Atoms	11

Software

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