8J0X
Crystal structure of horse spleen L-ferritin at -20deg Celsius.
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 293.15 | Ammonium sulfate (0.5-1.0M), Cadmium sulfate(12-20mM) |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
3.18 | 61.29 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 182.34 | α = 90 |
b = 182.34 | β = 90 |
c = 182.34 | γ = 90 |
Symmetry | |
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Space Group | F 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 | 253.15 | PIXEL | RIGAKU HyPix-6000HE | 2022-11-08 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU FR-E DW | 1.5420 |
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 | 1.6 | 22.286 | 98.9 | 0.065 | 0.073 | 0.031 | 0.998 | 15.6 | 4.7 | 34348 |
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 | 1.6 | 1.63 | 0.605 | 0.732 | 0.404 | 0.708 | 1.9 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | 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 | FREE R-VALUE | 1.6 | 22.286 | 34339 | 1712 | 98.684 | 0.149 | 0.1477 | 0.1687 | 14.359 |
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_6_deg | 17.256 |
r_dihedral_angle_3_deg | 15.096 |
r_dihedral_angle_2_deg | 8.046 |
r_lrange_it | 7.744 |
r_lrange_other | 7.743 |
r_scangle_it | 6.073 |
r_scangle_other | 6.07 |
r_dihedral_angle_1_deg | 5.196 |
r_scbond_it | 4.019 |
r_scbond_other | 4.017 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 1385 |
Nucleic Acid Atoms | |
Solvent Atoms | 161 |
Heterogen Atoms | 19 |
Software
Software | |
---|---|
Software Name | Purpose |
REFMAC | refinement |
CrysalisPro | data collection |
CrysalisPro | data reduction |
Aimless | data scaling |
MOLREP | phasing |
Coot | model building |