7N1L
Crystal Structure of Ribosomal-protein-alanine N-acetyltransferase from Brucella melitensis biovar Abortus 2308
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 8.5 | 287 | RigakuReagents JCSG+ screen, condition G1: 30% (V/V) Jeffamine ED-2003, 100mM HEPES free acid / sodium hydroxide pH 7.0: BrabA.17502.a.A1.PS01129 at 26mg/ml: tray 236060 G1: cryo: 20% EG: puck kzs9-7. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.84 | 56.7 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 67.02 | α = 87.121 |
b = 114.9 | β = 76.271 |
c = 122 | γ = 73.142 |
Symmetry | |
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Space Group | P 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 | CCD | ADSC QUANTUM 315r | 2012-10-18 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ALS BEAMLINE 5.0.1 | 0.97742 | ALS | 5.0.1 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | CC (Half) | 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 | 2.3 | 50 | 98.4 | 0.077 | 0.09 | 0.998 | 14.05 | 3.862 | 147858 | 42.519 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||
1 | 2.3 | 2.36 | 97.6 | 0.537 | 0.623 | 0.842 | 2.62 | 3.878 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | 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 | FREE R-VALUE | MR rosetta based on PDB entries 5F47, 6BVC, 5HMN, 2FE7, 3I9S, 3FYN, 2EUI, 1QSM, 3T9Y, 1Z4E, 1S3Z, 2R1I, 3JVN, 2DXQ, 5T7D, 3D8P, 4E04, 4EVY, 1MK4 | 2.3 | 48.73 | 1.98 | 147834 | 1756 | 98.4 | 0.2094 | 0.209 | 0.2484 | 0 | 52.25 |
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] | |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 13.3442 |
f_angle_d | 0.8934 |
f_chiral_restr | 0.0562 |
f_plane_restr | 0.009 |
f_bond_d | 0.0072 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 17210 |
Nucleic Acid Atoms | |
Solvent Atoms | 842 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
XDS | data reduction |
XSCALE | data scaling |
PHENIX | refinement |
PDB_EXTRACT | data extraction |
MR-Rosetta | phasing |
PHASER | phasing |
Coot | model building |
BUCCANEER | model building |