6KMK
Crystal structure of hydrogen peroxide bound bovine lactoperoxidase at 2.3 A resolution
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 4NT3 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6.8 | 298 | 0.2M AMMONIUM IODIDE, 20% PEG3350, pH 6.8, VAPOR DIFFUSION, HANGING DROP, 298K. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.39 | 48.63 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 53.828 | α = 90 |
b = 80.42 | β = 102.577 |
c = 75.823 | γ = 90 |
Symmetry | |
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Space Group | P 1 21 1 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | CCD | MARRESEARCH | 2019-07-11 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | RRCAT INDUS-2 BEAMLINE PX-BL21 | 0.9795 | RRCAT INDUS-2 | PX-BL21 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | CC (Half) | 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 | 2.3 | 54.515 | 99.2 | 0.112 | 0.96 | 7.2 | 3.4 | 27946 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 2.3 | 2.38 | 0.495 | 1 | 2 | 3.3 |
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 (All) | R-Work | R-Free | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 4NT3 | 2.3 | 54.46 | 27800 | 1401 | 98.725 | 0.248 | 0.2454 | 0.2951 | 40.537 |
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] | |
0.617 | -1.481 | -1.246 | 1.174 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 34.962 |
r_dihedral_angle_3_deg | 16.741 |
r_dihedral_angle_4_deg | 14.093 |
r_dihedral_angle_1_deg | 7.863 |
r_lrange_other | 7.101 |
r_lrange_it | 7.099 |
r_mcangle_it | 4.7 |
r_mcangle_other | 4.7 |
r_scangle_it | 4.328 |
r_scangle_other | 4.328 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4774 |
Nucleic Acid Atoms | |
Solvent Atoms | 251 |
Heterogen Atoms | 119 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
AUTOMAR | data reduction |
Aimless | data scaling |
MOLREP | phasing |