Experiment: 5JY4

A high magnesium structure of the isochorismate synthase, EntC

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3HWO

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	MICROBATCH	6.2	298.15	0.1 M MES pH 6.2, 50% PEG 200, 0.05 M ammonium chloride

Crystal Properties
Matthews coefficient	Solvent content
2.52	51.28

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 80.907	α = 90
b = 80.907	β = 90
c = 265.231	γ = 90

Symmetry
Space Group	P 41 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	Mirror: Rh coated	2016-02-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL12-2	0.979	SSRL	BL12-2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	2.11	38.9	99.7	0.074	0.999	14.5	7.4		51991

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.11	2.17	97.8		1.031	2	7.5

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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	FREE R-VALUE	3HWO	2.11	38.898	1.33	51881	2000	99.67	0.2026	0.2007	0.2047	0.2483	0.2502	Random selection	41.71

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]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	12.349
f_angle_d	1.273
f_chiral_restr	0.065
f_bond_d	0.014
f_plane_restr	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5790
Nucleic Acid Atoms
Solvent Atoms	140
Heterogen Atoms	34

Software

Software
Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHENIX	phasing