5AK8
Structure of C351A mutant of Porphyromonas gingivalis peptidylarginine deiminase
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 0.2M AMMONIUM SULFATE, 30% PEG5000MME, 0.1M MES PH 6.5 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.43 | 49.34 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 101.79 | α = 90 |
b = 84.09 | β = 92.64 |
c = 55.46 | γ = 90 |
Symmetry | |
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Space Group | C 1 2 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 | 2014-04-25 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I03 | Diamond | I03 |
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 | 1.48 | 64.8 | 95.3 | 0.06 | 10.4 | 3.4 | 73831 | 1 | 15.2 |
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 | 1.48 | 1.52 | 93.9 | 0.54 | 2.1 | 3.6 |
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 | 1.48 | 64.8 | 70193 | 3636 | 95.13 | 0.12921 | 0.12737 | 0.16444 | RANDOM | 19.703 |
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] | |
0.69 | -1.44 | -0.44 | -0.12 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_sphericity_free | 41.368 |
r_dihedral_angle_2_deg | 34.442 |
r_sphericity_bonded | 17.768 |
r_dihedral_angle_4_deg | 11.153 |
r_dihedral_angle_3_deg | 11.007 |
r_dihedral_angle_1_deg | 6.077 |
r_mcangle_it | 3.312 |
r_scbond_it | 3.206 |
r_mcbond_other | 2.644 |
r_mcbond_it | 2.643 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3288 |
Nucleic Acid Atoms | |
Solvent Atoms | 462 |
Heterogen Atoms | 90 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
PHASER | phasing |