1YLP
Atomic resolution structure of CTX-M-27 beta-lactamase
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1YLJ | PDB ENTRY 1YLJ |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 4.5 | 293 | ammonium sulfate, sodium acetate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K, pH 4.50 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
1.66 | 26.1 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 41.537 | α = 90 |
b = 62.784 | β = 90 |
c = 85.993 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 21 |
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 4 | MIRRORS | 2004-02-12 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ALS BEAMLINE 8.3.1 | ALS | 8.3.1 |
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 | 1.2 | 22 | 97.3 | 0.053 | 13.8 | 16.4 | 69072 | -3 |
Highest Resolution Shell | |||||||||||||||||||
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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 | 1.24 | 93.9 | 0.604 | 1.9 |
Refinement
Statistics | |||||||||||||||||||
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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 | PDB ENTRY 1YLJ | 1.2 | 20 | 65174 | 65174 | 2189 | 91.8 | 0.1318 | 0.132 | 0.132 | 0.158 | 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 |
30 | 1892 | 2295.37 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
s_zero_chiral_vol | 0.14 |
s_approx_iso_adps | 0.06 |
s_non_zero_chiral_vol | 0.042 |
s_from_restr_planes | 0.03 |
s_similar_adp_cmpnt | 0.026 |
s_angle_d | 0.02 |
s_anti_bump_dis_restr | 0.015 |
s_bond_d | 0.006 |
s_rigid_bond_adp_cmpnt | 0.004 |
s_similar_dist |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2076 |
Nucleic Acid Atoms | |
Solvent Atoms | 322 |
Heterogen Atoms | 63 |
Software
Software | |
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Software Name | Purpose |
SHELX | model building |
SHELXL-97 | refinement |
DENZO | data reduction |
SCALEPACK | data scaling |
SHELX | phasing |