Experiment: 6TV2

Heme d1 biosynthesis associated Protein NirF

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	10% (w/v) PEG 4000 20% (v/v)glycerol 0.03 NaNO3 0.03 Na2HPO4 0.03 (NH4)2SO4 0.1M MOPS/HEPES pH7.5

Crystal Properties
Matthews coefficient	Solvent content
2.39	48.62

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 101.129	α = 90
b = 147.83	β = 98.21
c = 108.716	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	100	PIXEL	DECTRIS PILATUS 6M-F		2018-05-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE X11	1	EMBL/DESY, HAMBURG	X11

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	1.561	107.6	94.7	0.067	0.995	6.4	3.7		289596

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.561	1.73	69.3		0.394	0.655	1.7	3.8

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	THROUGHOUT	6rte	1.561	59.46	1.34	289465	14291	64.86	0.1648	0.1628	0.1632	0.2024	0.2016	22.2603

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	23312
Nucleic Acid Atoms
Solvent Atoms	3569
Heterogen Atoms	104

Software

Software
Software Name	Purpose
Aimless	data scaling
STARANISO	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
DIALS	data reduction
PHASES	phasing