2P74
CTX-M-9 class A beta-lactamase apo crystal structure at 0.88 Angstrom resolution
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 | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 8.8 | 293 | potassium phosphate, pH 8.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.01 | 38.94 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 45.162 | α = 90 |
b = 106.796 | β = 102.09 |
c = 47.785 | γ = 90 |
Symmetry | |
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Space Group | P 1 21 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 4 | mirrors | 2005-04-08 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ALS BEAMLINE 8.3.1 | 0.800 | ALS | 8.3.1 |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 0.88 | 22 | 88.9 | 0.032 | 18.1 | 5.5 | 349567 | 310765 | -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) | |||||||||||
0.88 | 0.91 | 80.6 | 0.326 | 2.1 | 2.1 | 28059 |
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 | FREE R | pdb entry 1YLJ | 0.88 | 10 | 349495 | 297770 | 12801 | 85.2 | 0.1 | 0.1 | 0.1 | 0.1139 | 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 |
201 | 3805.05 | 4834.64 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
s_non_zero_chiral_vol | 0.112 |
s_zero_chiral_vol | 0.111 |
s_approx_iso_adps | 0.091 |
s_anti_bump_dis_restr | 0.054 |
s_similar_adp_cmpnt | 0.04 |
s_from_restr_planes | 0.0384 |
s_angle_d | 0.032 |
s_bond_d | 0.015 |
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 | 8679 |
Nucleic Acid Atoms | |
Solvent Atoms | 1001 |
Heterogen Atoms | 37 |
Software
Software | |
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Software Name | Purpose |
SHELX | model building |
SHELXL-97 | refinement |
HKL-2000 | data collection |
DENZO | data reduction |
SCALEPACK | data scaling |
SHELX | phasing |