3HML
Crystal Structure of PqqC Active Site Mutant H154S in Complex with PQQ
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1OTW | PDB ENTRY 1OTW |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7 | 293 | 1.0M Ammonium sulfate, 0.1M HEPES pH 7.0, 0.5% w/v Polyethylene glycol 8000, vapor diffusion, sitting drop, temperature 293K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.52 | 51.1 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 75.06 | ¦Á = 90 |
b = 118.291 | ¦Â = 90 |
c = 68.04 | ¦Ã = 90 |
Symmetry | |
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Space Group | P 21 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 | IMAGE PLATE | MAR555 FLAT PANEL | 2008-10-30 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | EMBL/DESY, HAMBURG BEAMLINE X11 | 0.8148 | EMBL/DESY, HAMBURG | X11 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | R Sym 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 | 2.35 | 39.44 | 99.7 | 0.107 | 0.099 | 13.6 | 6.7 | 25868 |
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) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
2.35 | 2.48 | 98.4 | 0.812 | 0.731 | 1.7 | 5.3 | 3640 |
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 | PDB ENTRY 1OTW | 2.35 | 38.37 | 25842 | 1311 | 99.58 | 0.215 | 0.212 | 0.261 | RANDOM | 46.347 |
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] | |
-0.31 | -0.03 | 0.35 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 32.308 |
r_dihedral_angle_4_deg | 17.059 |
r_dihedral_angle_3_deg | 16.905 |
r_dihedral_angle_1_deg | 6.597 |
r_scangle_it | 3.071 |
r_scbond_it | 2.121 |
r_angle_refined_deg | 1.696 |
r_mcangle_it | 1.533 |
r_mcbond_it | 0.949 |
r_nbtor_refined | 0.3 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3856 |
Nucleic Acid Atoms | |
Solvent Atoms | 57 |
Heterogen Atoms | 48 |
Software
Software | |
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Software Name | Purpose |
SCALA | data scaling |
MOLREP | phasing |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
MOSFLM | data reduction |