6YUS | pdb_00006yus

Capsule O-acetyltransferase of Neisseria meningitidis serogroup A H228A mutant in complex with CoA

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6YUQ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		291.15	Native H228A mutant CsaC crystallized in sitting drop setups at concentrations of 18 mg/ml. Fine screens around initial screening conditions resulted in many isomorphous crystals. Mother liquor contained 50 mM HEPES pH 7.0, 100 mM HEPES pH 7.6, 100 mM NaCl, 5 mM MgCl2, 1 mM EDTA, and 31-42% PEG200.

Crystal Properties
Matthews coefficient	Solvent content
2.82	56.34

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 136.74	α = 90
b = 136.74	β = 90
c = 70.76	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 PILATUS 6M-F		2018-10-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1)	0.976247	PETRA III, EMBL c/o DESY	P13 (MX1)

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	49.19	100	0.08	0.082	0.017	1	20.8	23.5		45806			64.033

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	2.13	99.9		4.501	4.662	1.1997	0.199	0.5	14.8

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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	6YUQ	2	49.16	1.33	44759	2239	97.72	0.1992	0.1975	0.21	0.24	0.24	77.54

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	17.6629
f_angle_d	1.1399
f_chiral_restr	0.0617
f_bond_d	0.0098
f_plane_restr	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3868
Nucleic Acid Atoms
Solvent Atoms	40
Heterogen Atoms	114

Software

Software
Software Name	Purpose
PHENIX	refinement
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
XSCALE	data scaling
PHASER	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.