4ZA4
Structure of A. niger Fdc1 with the prenylated-flavin cofactor in the iminium form.
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 277 | Initial screening of 0.3 microl 14 mg/ml A. niger Fdc1 in 100 mM NaCl, 25 mM Tris pH 7.5 and 0.3 microl reservoir solution at 4C resulted in a number of hits including PACT condition F4 (molecular dimensions). Seed stock produced from these crystals was used in an optimization screen based around 0.2 M potassium thiocyanate, Bis-Tris propane 6.5, 20 % w/v PEG 3350 mixing 0.05 microl seed stock, 0.25 microl protein solution and 0.3 microl reservoir solution at 4C. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.39 | 48.46 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 95.99 | ¦Á = 90 |
b = 63.93 | ¦Â = 90 |
c = 87.63 | ¦Ã = 90 |
Symmetry | |
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Space Group | P 21 21 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 | PIXEL | PSI PILATUS 6M | 2014-03-09 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I04 | 0.987 | Diamond | I04 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | Rpim I (All) | 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 | 1.22 | 33.82 | 99.96 | 0.037 | 11.2 | 6.1 | 152260 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | Rpim I (All) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1.22 | 1.25 | 99.99 | 0.354 | 2 | 5.8 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | 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 | 1.22 | 33.82 | 152260 | 8041 | 99.96 | 0.14652 | 0.14573 | 0.16111 | RANDOM | 9.809 |
Temperature Factor Modeling | ||||||
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Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
1.04 | -2.27 | 1.24 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 33.569 |
r_dihedral_angle_4_deg | 21.066 |
r_dihedral_angle_3_deg | 12.311 |
r_mcbond_other | 7.517 |
r_dihedral_angle_1_deg | 6.603 |
r_scangle_it | 6.569 |
r_rigid_bond_restr | 5.09 |
r_scbond_it | 4.873 |
r_angle_other_deg | 4.393 |
r_mcangle_it | 3.096 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3847 |
Nucleic Acid Atoms | |
Solvent Atoms | 447 |
Heterogen Atoms | 39 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
xia2 | data reduction |
xia2 | data scaling |
PHASER | phasing |