- PDB-7ck8: Crystal structure of human ferritin heavy chain mutant C90S/C102S... -
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Basic information
Entry
Database: PDB / ID: 7ck8
Title
Crystal structure of human ferritin heavy chain mutant C90S/C102S/C130S
Components
Ferritin heavy chain
Keywords
METAL TRANSPORT / iron storage / ferroxidase activity / nancage
Function / homology
Function and homology information
iron ion sequestering activity / : / autolysosome / Scavenging by Class A Receptors / Golgi Associated Vesicle Biogenesis / ferroxidase / intracellular sequestering of iron ion / ferroxidase activity / negative regulation of fibroblast proliferation / ferric iron binding ...iron ion sequestering activity / : / autolysosome / Scavenging by Class A Receptors / Golgi Associated Vesicle Biogenesis / ferroxidase / intracellular sequestering of iron ion / ferroxidase activity / negative regulation of fibroblast proliferation / ferric iron binding / Iron uptake and transport / ferrous iron binding / tertiary granule lumen / iron ion transport / intracellular iron ion homeostasis / ficolin-1-rich granule lumen / iron ion binding / immune response / negative regulation of cell population proliferation / Neutrophil degranulation / extracellular exosome / extracellular region / identical protein binding / membrane / nucleus / cytoplasm / cytosol Similarity search - Function
A: Ferritin heavy chain B: Ferritin heavy chain C: Ferritin heavy chain D: Ferritin heavy chain E: Ferritin heavy chain F: Ferritin heavy chain G: Ferritin heavy chain H: Ferritin heavy chain I: Ferritin heavy chain J: Ferritin heavy chain K: Ferritin heavy chain L: Ferritin heavy chain hetero molecules
A: Ferritin heavy chain B: Ferritin heavy chain C: Ferritin heavy chain D: Ferritin heavy chain E: Ferritin heavy chain F: Ferritin heavy chain G: Ferritin heavy chain H: Ferritin heavy chain I: Ferritin heavy chain J: Ferritin heavy chain K: Ferritin heavy chain L: Ferritin heavy chain hetero molecules
A: Ferritin heavy chain B: Ferritin heavy chain C: Ferritin heavy chain D: Ferritin heavy chain E: Ferritin heavy chain F: Ferritin heavy chain G: Ferritin heavy chain H: Ferritin heavy chain I: Ferritin heavy chain J: Ferritin heavy chain K: Ferritin heavy chain L: Ferritin heavy chain hetero molecules
Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 7, 2018
Radiation
Monochromator: DCM with Si(111) crystals / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.97905 Å / Relative weight: 1
Reflection
Resolution: 1.7→30 Å / Num. obs: 333244 / % possible obs: 100 % / Redundancy: 6.3 % / Biso Wilson estimate: 17.39 Å2 / CC1/2: 0.991 / CC star: 0.998 / Rmerge(I) obs: 0.131 / Rpim(I) all: 0.055 / Rrim(I) all: 0.143 / Χ2: 1.398 / Net I/av σ(I): 10.34 / Net I/σ(I): 6.3
Reflection shell
Diffraction-ID: 1
Resolution (Å)
Redundancy (%)
Rmerge(I) obs
Mean I/σ(I) obs
Num. unique obs
CC1/2
CC star
Rpim(I) all
Rrim(I) all
Χ2
% possible all
1.7-1.76
5.9
0.453
4.2
33065
0.934
0.983
0.204
0.498
1.114
99.9
1.76-1.83
5.5
0.371
5.08
33098
0.944
0.985
0.173
0.41
1.144
99.9
1.83-1.91
6.3
0.343
6.33
33169
0.959
0.99
0.148
0.374
1.16
100
1.91-2.02
6.3
0.291
7.64
33178
0.97
0.992
0.126
0.318
1.161
100
2.02-2.14
6.2
0.239
7.76
33217
0.971
0.992
0.105
0.262
1.106
100
2.14-2.31
6.3
0.204
9.67
33233
0.981
0.995
0.088
0.223
1.111
100
2.31-2.54
6.8
0.159
12.93
33328
0.988
0.997
0.066
0.173
1.078
100
2.54-2.91
6.5
0.131
13.55
33337
0.991
0.998
0.056
0.143
1.168
100
2.91-3.66
7
0.108
12.29
33536
0.994
0.999
0.044
0.117
1.727
100
3.66-30
6.5
0.089
9.73
34083
0.995
0.999
0.037
0.096
3.009
100
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Processing
Software
Name
Version
Classification
HKL-3000
datareduction
HKL-3000
datascaling
PHENIX
1.13_2998
refinement
PDB_EXTRACT
3.25
dataextraction
PHASER
phasing
Refinement
Method to determine structure: AB INITIO PHASING / Resolution: 1.8→28.976 Å / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 46.28 / Stereochemistry target values: ML Details: 1. bulk solvent correction 2. refinement of coordinates 3. refinement of ADPs 4. refinement of occupancies
Rfactor
Num. reflection
% reflection
Rfree
0.2225
13599
4.85 %
Rwork
0.1917
266585
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obs
0.1932
280184
99.47 %
Solvent computation
Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
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