4WHS
4-fluorocatechol bound to Protocatechuate 3,4-dioxygenase (pseudomonas putida) at pH 8.5
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 8.5 | 295 | 1.2 M Ammonium Sulfate, 2.5 mM 2-mercaptoethanol, 100 mM Tris-HCl pH 8.5; 2:1 ratio of well sol. to 40 mg/ml protein solution in drop |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.58 | 52.24 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 128.013 | α = 90 |
b = 140.665 | β = 90 |
c = 168.138 | γ = 90 |
Symmetry | |
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Space Group | I 2 2 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 315r | 2014-07-11 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 19-ID | 0.97918 | APS | 19-ID |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge 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 | 1.35 | 50 | 94.7 | 0.099 | 0.11 | 0.048 | 12.3 | 5.2 | 309614 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||
1 | 1.35 | 1.37 | 100 | 0.506 | 0.564 | 0.247 | 0.835 | 5.1 | 16283 |
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 | 3T63 | 1.35 | 29.55 | 294012 | 15583 | 94.55 | 0.1378 | 0.1362 | 0.1669 | RANDOM | 19.021 |
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] | |
1.2 | -0.68 | -0.52 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 31.135 |
r_sphericity_free | 26.363 |
r_dihedral_angle_4_deg | 16.488 |
r_dihedral_angle_3_deg | 12.299 |
r_sphericity_bonded | 9.455 |
r_dihedral_angle_1_deg | 6.649 |
r_rigid_bond_restr | 2.955 |
r_angle_refined_deg | 1.402 |
r_angle_other_deg | 0.801 |
r_chiral_restr | 0.086 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 10373 |
Nucleic Acid Atoms | |
Solvent Atoms | 1305 |
Heterogen Atoms | 164 |
Software
Software | |
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Software Name | Purpose |
HKL-3000 | data reduction |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
HKL-3000 | data scaling |
DENZO | data reduction |
SCALEPACK | data scaling |