1IMV
2.85 A crystal structure of PEDF
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1QLP | PDB entry 1QLP |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6.2 | 293 | 0.2M ammonium fluoride, 20% PEG 3350, pH 6.20, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.82 | 56.36 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 176.174 | α = 90 |
b = 62.514 | β = 90 |
c = 45.406 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 2 |
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 | 298 | IMAGE PLATE | RIGAKU RAXIS IIC | focusing mirrors | 2001-04-06 | M | SINGLE WAVELENGTH | |||||
2 | 1 | x-ray | 298 | IMAGE PLATE | RIGAKU RAXIS IIC | focusing mirrors | 2001-04-08 | M | SINGLE WAVELENGTH | |||||
3 | 1 | x-ray | 298 | IMAGE PLATE | RIGAKU RAXIS IIC | focusing mirrors | 2001-04-10 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU RU200 | 1.5418 | ||
2 | ROTATING ANODE | RIGAKU RU200 | 1.5418 | ||
3 | ROTATING ANODE | RIGAKU RU200 | 1.5418 |
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 | ||||||||
1,2,3 | 2.85 | 36.74 | 92.1 | 0.127 | 8.5 | 12.7 | 11214 | 11214 | 45.2 |
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) | |||||||||||
1,2,3 | 2.85 | 3.03 | 65.4 | 0.37 | 3 | 1166 |
Refinement
Statistics | |||||||||||||||||||
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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-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB entry 1QLP | 2.85 | 36.74 | 11241 | 11241 | 1167 | 91.2 | 0.188 | 0.227 | RANDOM | 31.4 |
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] | |
-3.92 | 7.44 | -3.52 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
c_dihedral_angle_d | 24.1 |
c_scangle_it | 2.98 |
c_mcangle_it | 2.19 |
c_scbond_it | 1.84 |
c_angle_deg | 1.3 |
c_mcbond_it | 1.25 |
c_improper_angle_d | 0.79 |
c_bond_d | 0.007 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2923 |
Nucleic Acid Atoms | |
Solvent Atoms | 45 |
Heterogen Atoms | 14 |
Software
Software | |
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Software Name | Purpose |
CNS | refinement |
DENZO | data reduction |
SCALEPACK | data scaling |
CNS | phasing |