6EVE
Structure of R175A S. cerevisiae Fdc1 with prFMN in the iminium form
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 4ZAC |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 277 | 0.1M sodium cacodylate pH 6.5, 0.25M Calcium Acetate, 15% PEG 4k |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.98 | 58.73 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 117.48 | α = 90 |
b = 98.64 | β = 97.24 |
c = 118.17 | γ = 90 |
Symmetry | |
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Space Group | P 1 21 1 |
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 | PIXEL | DECTRIS PILATUS 6M | 2015-07-12 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I04-1 | .928 | Diamond | I04-1 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 2.05 | 77.89 | 100 | 5.52 | 3.4 | 167153 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | Rrim I (All) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 2.05 | 2.134 | 1.071 | 2.9 |
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 | MOLECULAR REPLACEMENT | THROUGHOUT | 4ZAC | 2.05 | 77.89 | 158817 | 8336 | 99.7 | 0.1848 | 0.18265 | 0.22602 | RANDOM | 27.333 |
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] | |
0.01 | -1.47 | 2.29 | -1.87 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.835 |
r_dihedral_angle_4_deg | 19.794 |
r_dihedral_angle_3_deg | 14.88 |
r_dihedral_angle_1_deg | 6.573 |
r_long_range_B_refined | 5.845 |
r_long_range_B_other | 5.764 |
r_scangle_other | 4.374 |
r_scbond_other | 2.827 |
r_scbond_it | 2.826 |
r_mcangle_it | 2.814 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 15534 |
Nucleic Acid Atoms | |
Solvent Atoms | 1245 |
Heterogen Atoms | 152 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
xia2 | data reduction |
xia2 | data scaling |
REFMAC | phasing |