4M51
Crystal structure of amidohydrolase nis_0429 (ser145ala mutant) from nitratiruptor sp. sb155-2
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 7.5 | 0.1M HEPES:NAOH, PH 7.5, 0.2M LITHIUM SULFATE, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 294K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.33 | 47.03 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 92.163 | α = 90 |
b = 75.788 | β = 120.99 |
c = 76.291 | γ = 90 |
Symmetry | |
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Space Group | C 1 2 1 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | CCD | ADSC QUANTUM 315 | MIRRORS | 2013-07-18 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | NSLS BEAMLINE X29A | NSLS | X29A |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Sym 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 | 1.08 | 50 | 95.1 | 0.061 | 10.2 | 6.1 | 182346 | -5 |
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 | 1.08 | 1.1 | 91.1 | 0.64 | 2.5 | 6 |
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 | PDB ENTRY 3V7P | 1.08 | 33.91 | 176841 | 5505 | 95 | 0.118 | 0.117 | 0.135 | RANDOM | 16.48 |
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] | |
0.54 | 0.32 | -0.12 | -0.36 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_sphericity_free | 34.144 |
r_dihedral_angle_2_deg | 32.256 |
r_dihedral_angle_4_deg | 17.448 |
r_dihedral_angle_3_deg | 12.638 |
r_sphericity_bonded | 12.148 |
r_rigid_bond_restr | 8.752 |
r_dihedral_angle_1_deg | 6.337 |
r_long_range_B_refined | 5.463 |
r_long_range_B_other | 5.463 |
r_scbond_it | 4.509 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3183 |
Nucleic Acid Atoms | |
Solvent Atoms | 609 |
Heterogen Atoms | 30 |
Software
Software | |
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Software Name | Purpose |
PHASER | phasing |
REFMAC | refinement |
HKL-3000 | data reduction |
HKL-3000 | data scaling |