Experiment: 6XUB

Structure of coproheme decarboxylase from Corynebacterium diphteriae in complex with monovinyl monopropionyl deuteroheme

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293.15	PEG 33500, MgCl2

Crystal Properties
Matthews coefficient	Solvent content
2.2	43.98

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 60.969	α = 90
b = 123.382	β = 98.71
c = 78.009	γ = 90

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	170	PIXEL	DECTRIS PILATUS3 6M		2017-11-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID29	0.9762	ESRF	ID29

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.5645	48.1924	98.02	0.996	6.33	3.05		156754

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.5645	1.621	92.16		0.223

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	THROUGHOUT	3DTZ	1.78	48.1891	1.34	106562	5271	97.88	0.1764	0.1737	0.1783	0.2272	0.2294	44.0519

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]

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9310
Nucleic Acid Atoms
Solvent Atoms	737
Heterogen Atoms	385

Software

Software
Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
EDNA	data reduction
EDNA	data scaling
PHENIX	phasing