1HQD
PSEUDOMONAS CEPACIA LIPASE COMPLEXED WITH TRANSITION STATE ANALOGUE OF 1-PHENOXY-2-ACETOXY BUTANE
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3LIP | PDB entry code 3LIP |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7.4 | 278 | 12-45 % (v/v) MPD, 100 mM sodium citrate, 100 mM Hepes , pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 278K |
2 | VAPOR DIFFUSION, HANGING DROP | 8.6 | 278 | 15-36 % (v/v) n-propanol, 0.1 M Tris/HCl, pH 8.6, VAPOR DIFFUSION, HANGING DROP, temperature 278K |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 89.06 | α = 90 |
b = 46.63 | β = 120.86 |
c = 84.3 | 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 | IMAGE PLATE | MARRESEARCH | mirrors | 1999-06-15 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU | 1.5418 |
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 | 2.3 | 40 | 0.056 | 13473 | 12973 | 12.7 |
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) | |||||||||||
2.3 | 2.38 | 91.5 | 0.056 | 5.9 |
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 (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||
X-RAY DIFFRACTION | isomorphous replacement | THROUGHOUT | PDB entry code 3LIP | 2.3 | 10 | 12973 | 12797 | 1320 | 96.7 | 0.154 | 0.154 | 0.203 | RANDOM | 15.4 |
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] | |
0.07 | 0.22 | 2.78 | -2.85 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
c_dihedral_angle_d | 22.7 |
c_scangle_it | 1.52 |
c_scbond_it | 1.11 |
c_angle_deg | 1.1 |
c_mcangle_it | 1.09 |
c_mcbond_it | 0.69 |
c_improper_angle_d | 0.68 |
c_bond_d | 0.005 |
c_bond_d_na | |
c_bond_d_prot |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2338 |
Nucleic Acid Atoms | |
Solvent Atoms | 288 |
Heterogen Atoms | 16 |
Software
Software | |
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Software Name | Purpose |
DENZO | data reduction |
SCALEPACK | data scaling |
CNS | refinement |