6ZTC
CRYSTAL STRUCTURE OF PROSTAGLANDIN D2 SYNTHASE IN COMPLEX WITH FRAGMENT 1A AT 1.84A RESOLUTION.
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 8.4 | 293 | PEG6000, dioxane, TRIS-HCl, glycerol. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.43 | 49.36 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 49.071 | α = 90 |
b = 68.163 | β = 96.7 |
c = 68.517 | 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 | MAR scanner 345 mm plate | 2010-04-21 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU FR-E+ | 1.5418 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Sym I (Observed) | Rrim I (All) | Rpim I (All) | 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 | 1.84 | 21.054 | 97.4 | 0.06 | 0.071 | 0.037 | 13.3 | 3.6 | 37894 | 25.25 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Rrim I (All) | Rpim I (All) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||
1 | 1.84 | 1.94 | 94.5 | 0.485 | 0.485 | 0.57 | 0.297 | 1.6 | 3.5 |
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 | FOURIER SYNTHESIS | THROUGHOUT | Coordinates determined in-house | 1.84 | 20 | 35983 | 1890 | 97.03 | 0.1669 | 0.1637 | 0.2267 | RANDOM | 31.895 |
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] | |
-0.76 | 0.35 | -1.31 | 1.93 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 31.676 |
r_dihedral_angle_4_deg | 13.344 |
r_dihedral_angle_3_deg | 12.772 |
r_dihedral_angle_1_deg | 4.881 |
r_angle_refined_deg | 1.402 |
r_chiral_restr | 0.109 |
r_gen_planes_refined | 0.007 |
r_bond_refined_d | 0.006 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3296 |
Nucleic Acid Atoms | |
Solvent Atoms | 602 |
Heterogen Atoms | 99 |
Software
Software | |
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Software Name | Purpose |
MOSFLM | data processing |
SCALA | data scaling |
TRUNCATE | data reduction |
REFMAC | phasing |
REFMAC | refinement |
PDB_EXTRACT | data extraction |