2ZQD
Ceftazidime acyl-intermediate structure of class a beta-lact Toho-1 E166A/R274N/R276N triple mutant
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2ZQ7 | PDB ENTRY 2ZQ7 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 5.5 | 298 | 1.95-2.10M Ammonium sulfate, 0.2M sodium citrate, PH5.50, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.61 | 53.06 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 72.413 | ¦Á = 90 |
b = 72.413 | ¦Â = 90 |
c = 97.665 | ¦Ã = 120 |
Symmetry | |
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Space Group | P 32 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 | RIGAKU JUPITER 210 | mirrors | 2008-02-20 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SPRING-8 BEAMLINE BL26B1 | 0.7 | SPring-8 | BL26B1 |
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 | 1.19 | 50 | 100 | 0.056 | 42.97 | 10.4 | 95363 |
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) | |||||||||||
1.19 | 1.21 | 99.8 | 0.375 | 5.02 | 7.8 |
Refinement
Statistics | |||||||||||||||||||
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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 2ZQ7 | 1.19 | 50 | 90431 | 4777 | 99.97 | 0.13972 | 0.13869 | 0.1587 | RANDOM | 12.746 |
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] | |
-0.08 | -0.04 | -0.08 | 0.13 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 38.78 |
r_dihedral_angle_3_deg | 10.615 |
r_dihedral_angle_4_deg | 10.128 |
r_dihedral_angle_1_deg | 6.301 |
r_sphericity_free | 6.002 |
r_sphericity_bonded | 4.39 |
r_scangle_it | 3.6 |
r_scbond_it | 2.823 |
r_rigid_bond_restr | 1.943 |
r_mcangle_it | 1.827 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2181 |
Nucleic Acid Atoms | |
Solvent Atoms | 394 |
Heterogen Atoms | 51 |
Software
Software | |
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Software Name | Purpose |
MOLREP | phasing |
REFMAC | refinement |
HKL-2000 | data collection |
HKL-2000 | data reduction |
SCALEPACK | data scaling |