3F35
Apoferritin: complex with 2,6-diethylphenol
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
---|---|---|---|
Type | Source | Accession Code | Details |
experimental model | PDB | 1XZ1 | pdb entry 1XZ1 |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 291 | cadmium sulfate, ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
3.21 | 61.67 |
Crystal Data
Unit Cell | |
---|---|
Length ( ? ) | Angle ( ? ) |
a = 182.929 | ¦Á = 90 |
b = 182.929 | ¦Â = 90 |
c = 182.929 | ¦Ã = 90 |
Symmetry | |
---|---|
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 | 100 | CCD | MAR CCD 165 mm | 2006-04-16 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 17-ID | 1.0 | APS | 17-ID |
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 | 1.92 | 30 | 99.9 | 0.079 | 18.4 | 28.32 | 20594 | 20594 | 5.7 | 39.6 |
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) | |||||||||||
1.92 | 1.99 | 100 | 0.433 | 5.7 | 28.03 | 2006 |
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 | R-Free | R-Free Selection Details | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | FOURIER SYNTHESIS | THROUGHOUT | pdb entry 1XZ1 | 1.92 | 28.92 | 19288 | 1039 | 98.63 | 0.19254 | 0.19031 | 0.23573 | RANDOM | 33.461 |
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 | 36.663 |
r_dihedral_angle_4_deg | 17.416 |
r_dihedral_angle_3_deg | 13.408 |
r_scangle_it | 5.332 |
r_dihedral_angle_1_deg | 4.845 |
r_scbond_it | 3.48 |
r_mcangle_it | 1.881 |
r_angle_refined_deg | 1.751 |
r_mcbond_it | 1.138 |
r_chiral_restr | 0.122 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 1401 |
Nucleic Acid Atoms | |
Solvent Atoms | 135 |
Heterogen Atoms | 37 |
Software
Software | |
---|---|
Software Name | Purpose |
REFMAC | refinement |
d*TREK | data reduction |
d*TREK | data scaling |
REFMAC | phasing |