1V0Y
Phospholipase D from Streptomyces sp. strain PMF soaked with the substrate dibutyrylphosphatidylcholine.
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1F0I | BASED ON PDB ENTRY 1F0I |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 5.4 | 0.2 M NH4AC, 0.1 M CITRATE PHOSPHATE BUFFER AT PH5.4, 27.5% PEG 4000. CRYSTALS WERE THEREAFTER BACKSOAKED TWICE IN A PHOSPHATE- FREE BUFFER TO REMOVE TRACE-AMOUNTS OF PHOSPHATE., pH 5.40 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2 | 38.4 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 57.369 | α = 90 |
b = 56.462 | β = 93.74 |
c = 68.762 | 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 | IMAGE PLATE | MARRESEARCH | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE BM1A | ESRF | BM1A |
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 | 1.7 | 13.71 | 99.2 | 0.115 | 4.5 | 4.9 | 45138 |
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 | 1.7 | 1.8 | 92.9 | 0.473 | 2 | 4.6 |
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 | BASED ON PDB ENTRY 1F0I | 1.71 | 13.71 | 45138 | 2377 | 99.2 | 0.162 | 0.16 | 0.202 | RANDOM | 20.18 |
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] | |
-0.79 | -0.44 | 1.57 | -0.83 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_1_deg | 6.873 |
r_scangle_it | 4.269 |
r_scbond_it | 2.68 |
r_angle_refined_deg | 1.972 |
r_mcangle_it | 1.718 |
r_mcbond_it | 1.029 |
r_angle_other_deg | 0.979 |
r_symmetry_vdw_other | 0.284 |
r_nbd_refined | 0.253 |
r_nbd_other | 0.251 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3709 |
Nucleic Acid Atoms | |
Solvent Atoms | 413 |
Heterogen Atoms | 20 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
DENZO | data reduction |
SCALA | data scaling |
CNS | phasing |