2FFY
AmpC beta-lactamase N289A mutant in complex with a boronic acid deacylation transition state analog compound SM3
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1PI4 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 8.7 | 295 | POTASSIUM PHOSPHATE BUFFER, pH 8.7, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.52 | 51.11 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 118.84 | α = 90 |
b = 76.063 | β = 115.85 |
c = 97.898 | 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 | CCD | MARRESEARCH | mirrors | 2003-03-04 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 5ID-B | 0.97014 | APS | 5ID-B |
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 | 1.07 | 15 | 94.7 | 0.055 | 12.07 | 3.6 | 325964 | 325964 | -3 |
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) | |||||||||||
1.07 | 1.11 | 85.7 | 0.477 | 2.34 | 2.6 | 30545 |
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 | AB INITIO | FREE R | 1PI4 | 1.07 | 15 | 319468 | 319468 | 6552 | 92.9 | 0.1334 | 0.1334 | 0.1334 | 0.1635 | RANDOM |
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] | |
Coordinate Error | ||
---|---|---|
Structure Solution Method | Refinement High Resolution | Refinement Low Resolution |
279 | 5291.28 | 6570.99 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
s_zero_chiral_vol | 0.113 |
s_non_zero_chiral_vol | 0.112 |
s_approx_iso_adps | 0.059 |
s_anti_bump_dis_restr | 0.041 |
s_similar_adp_cmpnt | 0.034 |
s_from_restr_planes | 0.0307 |
s_angle_d | 0.029 |
s_bond_d | 0.013 |
s_rigid_bond_adp_cmpnt | 0.005 |
s_similar_dist |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 12639 |
Nucleic Acid Atoms | |
Solvent Atoms | 1173 |
Heterogen Atoms | 74 |
Software
Software | |
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Software Name | Purpose |
XDS | data scaling |
XDS | data reduction |
SHELX | model building |
SHELXL-97 | refinement |
SHELX | phasing |