4N4N
Nitrosomonas europea HAO
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1FGJ | PDB ENTRY 1FGJ |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | MICROBATCH UNDER OIL | 7.5 | 293 | 42% v/v PEG400, 50 mM potassium nitrate, 100 mM MES/NaOH, pH 7.5, MICROBATCH UNDER OIL, temperature 293K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.78 | 55.82 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 140.72 | ¦Á = 90 |
b = 141.97 | ¦Â = 90 |
c = 106.72 | ¦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 | two horizontal deflecting and one vertical deflecting X-ray mirror | 2012-12-01 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | PETRA III, DESY BEAMLINE P11 | 0.9786 | PETRA III, DESY | P11 |
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 | 2.2 | 50.4 | 99.5 | 0.102 | 13.6 | 5.6 | 98124 | 98124 |
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 | 2.2 | 2.3 | 99.3 | 0.588 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB ENTRY 1FGJ | 2.2 | 50.4 | 98124 | 98124 | 10263 | 99.97 | 0.18246 | 0.18246 | 0.17928 | 0.21273 | RANDOM | 29.017 |
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] | |
-2.15 | 0.26 | 1.89 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 33.164 |
r_dihedral_angle_4_deg | 17.906 |
r_dihedral_angle_3_deg | 14.63 |
r_dihedral_angle_1_deg | 5.055 |
r_scangle_it | 1.124 |
r_angle_refined_deg | 1.025 |
r_scbond_it | 0.723 |
r_mcangle_it | 0.536 |
r_mcbond_it | 0.283 |
r_chiral_restr | 0.07 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 13309 |
Nucleic Acid Atoms | |
Solvent Atoms | 1094 |
Heterogen Atoms | 1038 |
Software
Software | |
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Software Name | Purpose |
HEIDI | data collection |
PHASER | phasing |
REFMAC | refinement |
XDS | data reduction |
XSCALE | data scaling |