5JKK | pdb_00005jkk

Crystal structure of the negatively supercharged variant Ftn(neg) of human heavy chain ferritin

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2CEI

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	0.52 M magnesium acetate, 100 mM Tris, pH 8.5, 8 mg/mL Ftn(neg)

Crystal Properties
Matthews coefficient	Solvent content
2.89	57.46

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 180.98	α = 90
b = 180.98	β = 90
c = 180.98	γ = 90

Symmetry
Space Group	P 2 3

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 2M-F		2015-06-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06DA	1.00	SLS	X06DA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.6	48.37	99.9	0.0474	40.93	13.17		255788			9.56

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	1.6	1.7	99.3		0.194	11.21	11.16

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	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	THROUGHOUT	2CEI	1.6	48.37	243300	12488	99.87	0.1247	0.1238	0.1405	0.1429	0.157	RANDOM	10.97

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
r_dihedral_angle_2_deg	41.241
r_dihedral_angle_4_deg	18.279
r_dihedral_angle_3_deg	11.373
r_dihedral_angle_1_deg	5.278
r_angle_refined_deg	2.164
r_mcangle_it	1.526
r_mcbond_it	1.066
r_mcbond_other	1.053
r_angle_other_deg	0.942
r_chiral_restr	0.135
r_bond_refined_d	0.024
r_gen_planes_refined	0.014
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	11376
Nucleic Acid Atoms
Solvent Atoms	1681
Heterogen Atoms	29

Software

Software
Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction