2ZZX
Crystal Structure of a Periplasmic Substrate Binding Protein in Complex with Lactate
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2ZZV | PDB ENTRY 2ZZV |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 293 | 0.05M Potassium phosphate monobasic, 20% PEG8000, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.29 | 46.33 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 162.792 | α = 90 |
b = 103.501 | β = 101.86 |
c = 90.76 | 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 | ADSC QUANTUM 315 | 2006-11-17 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SPRING-8 BEAMLINE BL41XU | 1.0000 | SPring-8 | BL41XU |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Sym 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 | 1.75 | 50 | 90.1 | 0.059 | 18.9 | 3.3 | 133774 | 16.2 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 1.75 | 1.81 | 71 | 0.207 | 3.3 | 1.8 | 10504 |
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 2ZZV | 1.75 | 45.29 | 133460 | 6789 | 90.1 | 0.177 | 0.177 | 0.207 | RANDOM | 23.6 |
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] | |
-1.3 | -0.08 | -0.25 | 1.55 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
c_dihedral_angle_d | 22.3 |
c_scangle_it | 3.84 |
c_scbond_it | 2.73 |
c_mcangle_it | 2.41 |
c_mcbond_it | 1.81 |
c_angle_deg | 1.4 |
c_improper_angle_d | 0.91 |
c_bond_d | 0.009 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 10529 |
Nucleic Acid Atoms | |
Solvent Atoms | 921 |
Heterogen Atoms | 47 |
Software
Software | |
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Software Name | Purpose |
CNS | refinement |
HKL-2000 | data collection |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
MOLREP | phasing |