4KJT
Structure of the L100F MUTANT OF DEHALOPEROXIDASE-HEMOGLOBIN A FROM AMPHITRITE ORNATA WITH OXYGEN
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1EWA |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6.5 | 277 | 28-32% PEG4K, .2M ammonium sulfate, .02M sodium cacodylate, pH 6.5, vapor diffusion, hanging drop, temperature 277K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.19 | 43.85 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 59.128 | α = 90 |
b = 67.782 | β = 90 |
c = 68.132 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 21 |
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 | MARMOSAIC 325 mm CCD | 2012-06-09 | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 22-ID | 1.0 | APS | 22-ID |
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 | 1.44 | 50 | 98.3 | 0.064 | 15 | 6.9 | 50814 | 49939 | 1 | 1 |
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) | |||||||||||
1 | 1.44 | 1.46 | 68.9 | 0.357 | 4.7 | 1706 |
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 | 1EWA | 1.44 | 48.05 | 50446 | 49870 | 2538 | 98.81 | 0.196 | 0.1351 | 0.1328 | 0.1803 | RANDOM | 20.5499 |
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] | |
0.52 | -0.31 | -0.21 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_sphericity_free | 37.898 |
r_dihedral_angle_2_deg | 37.028 |
r_dihedral_angle_4_deg | 15.4 |
r_dihedral_angle_3_deg | 13.515 |
r_sphericity_bonded | 13.343 |
r_rigid_bond_restr | 5.859 |
r_dihedral_angle_1_deg | 4.855 |
r_mcangle_it | 3.422 |
r_mcbond_it | 2.929 |
r_mcbond_other | 2.926 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2159 |
Nucleic Acid Atoms | |
Solvent Atoms | 355 |
Heterogen Atoms | 102 |
Software
Software | |
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Software Name | Purpose |
DENZO | data reduction |
SCALEPACK | data scaling |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
SERGUI | data collection |