2DU2
Crystal Structure Analysis of the L-Lactate Oxidase
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1GOX | PDB ENTRY 1GOX |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 8 | 298 | 18-20%(w/v) PEG 8000, 50mM Tris buffer pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.7 | 54.51 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 191.096 | α = 90 |
b = 191.096 | β = 90 |
c = 194.497 | γ = 90 |
Symmetry | |
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Space Group | I 4 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 4 | 2004-12-10 | M | SINGLE WAVELENGTH | ||||||
2 | 1 | 100 | IMAGE PLATE | MAC Science, DIP6040 | ||||||||||
3 | 1 | 100 | CCD | MARRESEARCH | ||||||||||
4 | 1 | 100 | CCD | ADSC QUANTUM 4 |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SPRING-8 BEAMLINE BL38B1 | 1.0 | SPring-8 | BL38B1 |
2 | SYNCHROTRON | SPRING-8 BEAMLINE BL44XU | 1.0 | SPring-8 | BL44XU |
3 | SYNCHROTRON | SPRING-8 BEAMLINE BL41XU | 1.0 | SPring-8 | BL41XU |
4 | SYNCHROTRON | PHOTON FACTORY BEAMLINE AR-NW12A | 1.0 | Photon Factory | AR-NW12A |
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 | 2.07 | 46 | 100 | 0.142 | 22.72 | 12.8 | 108566 | 108566 | 1 | 1 | 19.47 |
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) | |||||||||||
2.07 | 2.14 | 100 | 0.436 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (I) | Cut-off Sigma (F) | 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 1GOX | 2.1 | 20 | 1 | 1 | 103006 | 103006 | 5418 | 100 | 0.16168 | 0.16168 | 0.1597 | 0.19904 | RANDOM | 19.443 |
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] | |
0.32 | 0.32 | -0.64 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 37.092 |
r_dihedral_angle_4_deg | 17.615 |
r_dihedral_angle_3_deg | 16.219 |
r_dihedral_angle_1_deg | 6.865 |
r_scangle_it | 4.002 |
r_scbond_it | 2.639 |
r_angle_refined_deg | 1.781 |
r_mcangle_it | 1.587 |
r_mcbond_it | 1.007 |
r_nbtor_refined | 0.312 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 11552 |
Nucleic Acid Atoms | |
Solvent Atoms | 1109 |
Heterogen Atoms | 124 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
HKL-2000 | data reduction |
SCALEPACK | data scaling |
AMoRE | phasing |