4EXQ
CRYSTAL STRUCTURE of UROPORPHYRINOGEN DECARBOXYLASE (UPD) FROM BURKHOLDERIA THAILANDENSIS E264
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7 | 289 | EBS INTERNAL TRACKING NUMBER HEPES (PH 7.0), 500 MM NACL, 2 MM DTT, 0.025% SODIUM AZIDE, 5% GLYCEROL, 0.4 UL X 0.4 UL DROP WITH 10% PEG 1000, 10% PEG 8000, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.23 | 44.81 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 53.32 | ¦Á = 90 |
b = 53.32 | ¦Â = 90 |
c = 233.62 | ¦Ã = 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 210 | 2012-04-21 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ALS BEAMLINE 5.0.1 | 0.9774 | ALS | 5.0.1 |
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 | 1.65 | 50 | 99.6 | 0.061 | 16.26 | 41883 | -3 | 25.07 |
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 | 1.65 | 1.69 | 99.9 | 0.521 | 2.9 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | 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 | 1.65 | 50 | 41768 | 2105 | 0.179 | 0.178 | 0.2 | RANDOM | 19.86 |
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] | |
0.75 | 0.75 | -1.5 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 32.257 |
r_dihedral_angle_4_deg | 20.776 |
r_dihedral_angle_3_deg | 12.643 |
r_dihedral_angle_1_deg | 5.41 |
r_angle_refined_deg | 1.315 |
r_chiral_restr | 0.088 |
r_bond_refined_d | 0.01 |
r_gen_planes_refined | 0.007 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2678 |
Nucleic Acid Atoms | |
Solvent Atoms | 174 |
Heterogen Atoms | 1 |
Software
Software | |
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Software Name | Purpose |
PHASER | phasing |
REFMAC | refinement |