6TSF
Crystal structure of human L ferritin (HuLf) Fe(III)-loaded for 60 minutes
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
---|---|---|---|
Type | Source | Accession Code | Details |
experimental model | PDB | 5LG8 |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 4.6 | 293 | 80 mM cadmium nitrate, 80 mM ammonium sulfate, 200 mM sodium acetate, pH 4.6 |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
3.59 | 65.72 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 151.14 | α = 90 |
b = 151.14 | β = 90 |
c = 151.14 | γ = 90 |
Symmetry | |
---|---|
Space Group | I 4 3 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 PILATUS3 6M | 2018-02-19 | M | MAD | ||||||
2 | 1 | x-ray | 100 | PIXEL | DECTRIS PILATUS3 6M | 2018-02-19 | M | MAD | ||||||
3 | 1 | x-ray | 100 | PIXEL | DECTRIS PILATUS3 6M | 2018-02-19 | M | MAD |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I03 | 0.97622 | Diamond | I03 |
2 | SYNCHROTRON | DIAMOND BEAMLINE I03 | 1.73891 | Diamond | I03 |
3 | SYNCHROTRON | DIAMOND BEAMLINE I03 | 1.74478 | Diamond | I03 |
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 | 2.09 | 106.87 | 93.5 | 0.065 | 0.069 | 0.015 | 1 | 26.8 | 20.3 | 16631 | 2 | 42.6 |
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 | 2.09 | 2.2 | 100 | 0.849 | 0.887 | 0.19 | 0.925 | 3.7 | 21.5 |
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 (All) | R-Work | R-Free | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 5LG8 | 2.09 | 47.84 | 16500 | 823 | 92.848 | 0.211 | 0.2087 | 0.252 | 44.84 |
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 | 37.38 |
r_dihedral_angle_4_deg | 25.739 |
r_dihedral_angle_3_deg | 17.642 |
r_lrange_it | 11.001 |
r_lrange_other | 10.848 |
r_scangle_it | 8.946 |
r_scangle_other | 8.945 |
r_scbond_it | 6.323 |
r_scbond_other | 6.319 |
r_dihedral_angle_1_deg | 5.857 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 1382 |
Nucleic Acid Atoms | |
Solvent Atoms | 145 |
Heterogen Atoms | 17 |
Software
Software | |
---|---|
Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
SCALA | data scaling |
MOLREP | phasing |