4USC
Crystal structure of peroxidase from palm tree Chamaerops excelsa
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3HDL | PDB ENTRY 3HDL |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 0.17 M AMMONIUM SULFATE, 0.085 M TRIS PH 8.0, 17% PEG MME 2K, 15% GLYCEROL |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.11 | 42 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 70.18 | ¦Á = 90 |
b = 100.65 | ¦Â = 90 |
c = 132.31 | ¦Ã = 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 | 2011-05-13 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | LNLS BEAMLINE W01B-MX2 | LNLS | W01B-MX2 |
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 | 2.6 | 80.1 | 90.1 | 0.01 | 10.4 | 4.3 | 29525 | 3.7 |
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 | 2.6 | 2.69 | 91.8 | 0.56 | 3.7 | 4.3 |
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 3HDL | 2.6 | 80.11 | 25246 | 1369 | 90.14 | 0.21964 | 0.21816 | 0.24585 | RANDOM | 54.787 |
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] | |
-4.23 | 10.61 | -6.38 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 40.535 |
r_dihedral_angle_4_deg | 19.198 |
r_dihedral_angle_3_deg | 14.934 |
r_dihedral_angle_1_deg | 5.849 |
r_mcangle_it | 3.506 |
r_scbond_it | 2.948 |
r_angle_other_deg | 2.633 |
r_mcbond_other | 2.211 |
r_mcbond_it | 2.21 |
r_angle_refined_deg | 1.731 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4461 |
Nucleic Acid Atoms | |
Solvent Atoms | 85 |
Heterogen Atoms | 314 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
XDS | data scaling |
PHASER | phasing |