4ML5
one minute iron loaded frog M ferritin mutant H54Q
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3KA3 | pdb entry 3KA3 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 9 | 277 | 1.6-2M magnesium chloride, 0.1M bicine, pH 9, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.16 | 61.07 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 184.23 | α = 90 |
b = 184.23 | β = 90 |
c = 184.23 | γ = 90 |
Symmetry | |
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Space Group | F 4 3 2 |
Diffraction
Diffraction Experiment | ||||||||||||||
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ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | CCD | MARMOSAIC 225 mm CCD | mirror | 2012-10-08 | M | SINGLE WAVELENGTH | |||||
2 | 1 | x-ray | PIXEL | DECTRIS PILATUS 2M | mirror | 2012-10-29 | M | MAD |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE BM14 | 0.954 | ESRF | BM14 |
2 | SYNCHROTRON | ELETTRA BEAMLINE 5.2R | 1.751, 1.739 | ELETTRA | 5.2R |
Data Collection
Overall | |||||||||||||||||||
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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 | ||||||||
1,2 | 1.22 | 22.51 | 100 | 0.082 | 17.9 | 13.5 | 1071136 | 79449 | 2 | 8.162 |
Highest Resolution Shell | |||||||||||||||||||
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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) | |||||||||||
1,2 | 1.22 | 1.29 | 100 | 0.375 | 5.1 | 8.6 | 11391 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (I) | Number Reflections (All) | 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 | MOLECULAR REPLACEMENT | THROUGHOUT | pdb entry 3KA3 | 1.22 | 21.71 | 2 | 75437 | 75437 | 3987 | 99.96 | 0.13976 | 0.13904 | 0.15352 | RANDOM | 9.357 |
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 | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 39.169 |
r_dihedral_angle_4_deg | 18.699 |
r_sphericity_free | 14.237 |
r_dihedral_angle_3_deg | 13.492 |
r_sphericity_bonded | 4.594 |
r_dihedral_angle_1_deg | 4.546 |
r_rigid_bond_restr | 4.202 |
r_angle_refined_deg | 1.037 |
r_angle_other_deg | 0.841 |
r_chiral_restr | 0.058 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1429 |
Nucleic Acid Atoms | |
Solvent Atoms | 382 |
Heterogen Atoms | 29 |
Software
Software | |
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Software Name | Purpose |
MOLREP | phasing |
REFMAC | refinement |
MOSFLM | data reduction |
SCALA | data scaling |