5JWL
Factor Inhibiting HIF D201E in Complex with Zn, and Alpha-Ketoglutarate
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3D8C |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7.5 | 293 | 0.1M Hepes, 1.6mM ammonium sulfate, 3% PEG 400 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.41 | 63.9 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 86.131 | α = 90 |
b = 86.131 | β = 90 |
c = 149.213 | γ = 90 |
Symmetry | |
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Space Group | P 41 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 | 100 | CCD | ADSC QUANTUM 270 | FOCUSING MIRRORS | 2013-10-03 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | NSLS BEAMLINE X6A | 1.08 | NSLS | X6A |
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 | 2.4 | 50 | 98.2 | 0.131 | 9.2 | 9 | 22314 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||||
1 | 2.4 | 2.44 | 100 | 9.5 |
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 | 3D8C | 2.4 | 32.56 | 18715 | 1592 | 89.54 | 0.1839 | 0.1803 | 0.2259 | RANDOM | 67.601 |
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] | |
-1.03 | -1.03 | 2.06 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 40.475 |
r_dihedral_angle_4_deg | 19.017 |
r_dihedral_angle_3_deg | 17.13 |
r_dihedral_angle_1_deg | 7.254 |
r_mcangle_it | 6.334 |
r_mcbond_it | 4.251 |
r_mcbond_other | 4.251 |
r_angle_refined_deg | 1.755 |
r_angle_other_deg | 0.889 |
r_chiral_restr | 0.101 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2798 |
Nucleic Acid Atoms | |
Solvent Atoms | 114 |
Heterogen Atoms | 28 |
Software
Software | |
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Software Name | Purpose |
HKL-2000 | data collection |
HKL-2000 | data scaling |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
HKL-2000 | data reduction |
PHASER | phasing |