2E9E
Crystal structure of the complex of goat lactoperoxidase with Nitrate at 3.25 A resolution
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2GJ1 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 8.2 | 280 | TRIS HYDROCHLORIDE, pH 8.2, VAPOR DIFFUSION, HANGING DROP, temperature 280K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.54 | 51.54 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 58.522 | α = 85.3 |
b = 72.537 | β = 84.06 |
c = 83.983 | γ = 75.68 |
Symmetry | |
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Space Group | P 1 |
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 | 278 | IMAGE PLATE | MARRESEARCH | Mirror | 2006-09-18 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU RU300 | 1.414 |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 3.25 | 20 | 95.2 | 0.154 | 3.8 | 19863 | 19863 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 3.25 | 3.31 | 95.8 | 0.278 | 1.9 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 (Depositor) | R-Free (Depositor) | R-Free Selection Details | Mean Isotropic B | ||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 2GJ1 | 3.25 | 20 | 19863 | 18734 | 1008 | 94.85 | 0.17214 | 0.17123 | 0.16868 | 0.20343 | RANDOM | 18.726 |
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] | |
2.5 | 1.82 | 0.21 | -0.85 | 0.13 | -2.62 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 39.971 |
r_dihedral_angle_3_deg | 18.537 |
r_dihedral_angle_4_deg | 17.42 |
r_dihedral_angle_1_deg | 4.833 |
r_scangle_it | 3.379 |
r_mcangle_it | 1.919 |
r_scbond_it | 1.916 |
r_angle_refined_deg | 1.59 |
r_mcbond_it | 1.011 |
r_nbtor_refined | 0.323 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 9508 |
Nucleic Acid Atoms | |
Solvent Atoms | 380 |
Heterogen Atoms | 411 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
AUTOMAR | data reduction |
SCALEPACK | data scaling |
AMoRE | phasing |