1BEH
HUMAN PHOSPHATIDYLETHANOLAMINE BINDING PROTEIN IN COMPLEX WITH CACODYLATE
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1BD9 | PDB ENTRY 1BD9 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 6.5 | PROTEIN WAS CRYSTALLIZED FROM 28-32% PEG 4000/6000/8000, 200-300 MM SODIUM ACETATE, 100MM SODIUM CACODYLATE., pH 6.5 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.2 | 36 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 45.43 | α = 90 |
b = 61.63 | β = 101.09 |
c = 67.92 | 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 | MIRRORS | 1997-04-15 | M |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SRS BEAMLINE PX7.2 | SRS | PX7.2 |
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 | 20 | 95.6 | 0.055 | 16.2 | 2.4 | 38803 | -3 | 19.1 |
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) | |||||||||||
1 | 1.7 | 1.76 | 94.9 | 0.28 | 2.6 | 2.3 |
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-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB ENTRY 1BD9 | 1.75 | 20 | 33851 | 1773 | 95 | 0.235 | 0.286 | SHELLS | 24 |
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] | |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
p_transverse_tor | 22 |
p_staggered_tor | 15.7 |
p_planar_tor | 3.7 |
p_scangle_it | 1.9 |
p_mcangle_it | 1.6 |
p_scbond_it | 1.2 |
p_mcbond_it | 1.1 |
p_multtor_nbd | 0.239 |
p_singtor_nbd | 0.172 |
p_chiral_restr | 0.111 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2919 |
Nucleic Acid Atoms | |
Solvent Atoms | 239 |
Heterogen Atoms | 10 |
Software
Software | |
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Software Name | Purpose |
AMoRE | phasing |
REFMAC | refinement |
DENZO | data reduction |
SCALEPACK | data scaling |