3K4J
Pyranose 2-oxidase H450Q mutant
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2IGO | pdb entry 2IGO |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 5.2 | 298 | 0.1M MES, 50MM MGCL2, 10% (W/V)% MONOMETHYLETHER PEG 2000, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.25 | 45.42 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 101.91 | ¦Á = 90 |
b = 101.91 | ¦Â = 90 |
c = 120.47 | ¦Ã = 90 |
Symmetry | |
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Space Group | P 42 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 | MARRESEARCH | MIRRORS | 2008-10-26 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | MAX II BEAMLINE I911-2 | 1.0379 | MAX II | I911-2 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 30 | 99.8 | 0.187 | 17.3 | 14.5 | 43397 | 43397 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 2 | 2.1 | 99.9 | 0.859 | 5.2 | 14.5 | 5784 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | pdb entry 2IGO | 2 | 29.2 | 41420 | 41420 | 1990 | 99.89 | 0.15842 | 0.15842 | 0.15643 | 0.19956 | RANDOM | 11.138 |
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] | |
-0.29 | -0.29 | 0.59 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 37.606 |
r_dihedral_angle_4_deg | 14.494 |
r_dihedral_angle_3_deg | 13.618 |
r_dihedral_angle_1_deg | 6.875 |
r_scangle_it | 3.871 |
r_scbond_it | 2.843 |
r_angle_refined_deg | 1.861 |
r_mcangle_it | 1.694 |
r_mcbond_it | 1.393 |
r_angle_other_deg | 1.011 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4517 |
Nucleic Acid Atoms | |
Solvent Atoms | 307 |
Heterogen Atoms | 65 |
Software
Software | |
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Software Name | Purpose |
MAR345 | data collection |
PHASER | phasing |
REFMAC | refinement |
XDS | data reduction |
XSCALE | data scaling |