2C18
5-(4-Carboxy-2-oxo-butane-1-sulfonyl)-4-oxo-pentanoic acid bound to Porphobilinogen synthase from Pseudomonas aeruginosa
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
---|---|---|---|
Type | Source | Accession Code | Details |
experimental model | PDB | 1B4K | PDB ENTRY 1B4K |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7.5 | HANGING DROP IN 24-WELL LIMBRO PLATES. DROPS MADE OF 5 MICROLITRES PROTEIN SOLUTION, 10 MG/ML PROTEIN, 50 MM TRIS-HCL, PH 7.5, 5 MM MGCL2, 10 MM 5-(4-CARBOXY-2-OXO-BUTANE-1-SULFONYL)-4-OXO-PENTANOIC ACID DISODIUM SALT) PLUS 5 MICROL RESERVOIR SOLUTION (31.0 % (V/V) PEG-400, 100 MM NA-HEPES PH 7.5, 180 MM MGCL2) ABOVE 500 MICROL OF RESERVOIR SOLUTION. |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
2.3 | 45.4 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 125.596 | α = 90 |
b = 125.596 | β = 90 |
c = 86.573 | γ = 90 |
Symmetry | |
---|---|
Space Group | P 4 21 2 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | CCD | MARRESEARCH | MIRRORS | 2005-02-09 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | BESSY BEAMLINE 14.1 | BESSY | 14.1 |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 1.93 | 39.5 | 95 | 0.12 | 11.7 | 6.1 | 55920 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 1.93 | 1.98 | 93.4 | 0.48 | 3.46 | 5.5 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | PDB ENTRY 1B4K | 1.93 | 89.8 | 47003 | 2515 | 94.3 | 0.151 | 0.149 | 0.186 | RANDOM | 19.11 |
Temperature Factor Modeling | ||||||
---|---|---|---|---|---|---|
Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
0.09 | 0.09 | -0.18 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.08 |
r_dihedral_angle_4_deg | 19.034 |
r_dihedral_angle_3_deg | 14.31 |
r_dihedral_angle_1_deg | 8.678 |
r_scangle_it | 3.518 |
r_scbond_it | 2.197 |
r_angle_refined_deg | 1.469 |
r_mcangle_it | 1.24 |
r_mcbond_it | 0.706 |
r_nbtor_refined | 0.297 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 5155 |
Nucleic Acid Atoms | |
Solvent Atoms | 639 |
Heterogen Atoms | 31 |
Software
Software | |
---|---|
Software Name | Purpose |
REFMAC | refinement |
DENZO | data reduction |
SCALEPACK | data scaling |