Experiment: 6P8L

Escherichia coli Bacterioferritin Substituted with Zinc Protoporphyrin IX (Zn Absorption Edge X-ray Data)

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6P8K	PDB entry 6P8K

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6	295	2.4 M sodium malonate, pH 6.0

Crystal Properties
Matthews coefficient	Solvent content
3.49	64.75

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 207.918	α = 90
b = 207.918	β = 90
c = 143.046	γ = 90

Symmetry
Space Group	P 42 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		2018-02-02	M	SINGLE WAVELENGTH
2	1	x-ray	100	PIXEL	DECTRIS PILATUS 6M-F		2018-02-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 24-ID-C	1.2822	APS	24-ID-C
2	SYNCHROTRON	APS BEAMLINE 24-ID-C	1.3190	APS	24-ID-C

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	2.1	92.65	99.8	0.169	0.182	0.067	0.998	8.2	7.3		179257			30.16

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	2.1	2.21	99.9		1.777	1.908	0.972	0.699	1.1	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)	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	THROUGHOUT	PDB entry 6P8K	2.1	92.65	1.97	344368	3852	99.17	0.2132	0.2129	0.2155	0.2402	0.2431	35.55

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	17.7105
f_angle_d	1.9718
f_chiral_restr	0.0622
f_bond_d	0.0068
f_plane_restr	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	15528
Nucleic Acid Atoms
Solvent Atoms	1598
Heterogen Atoms	470

Software

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