3NIU
Crystal structure of the complex of dimeric goat lactoperoxidase with diethylene glycol at 2.9 A resolution
X-RAY DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 2OJV | |
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 4.8 | 280 | 0.2M Potassium dihydrogen phosphate 20%w/v PEG 3350, PH 4.8, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 280K |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.57 | 52.09 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( ? ) | Angle ( ? ) |
| a = 59.199 | ¦Á = 79.93 |
| b = 75.587 | ¦Â = 77.86 |
| c = 83.808 | ¦Ã = 72.5 |
| Symmetry | |
|---|---|
| Space Group | P 1 |
Diffraction
| Diffraction Experiment | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 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 | 2006-09-20 | M | SINGLE WAVELENGTH | |||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | ROTATING ANODE | RIGAKU RU300 | 1.5418 | ||
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 2.94 | 25 | 96 | 4 | 28536 | 28536 | |||||||||||||
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 | R-Free | R-Free Selection Details | Mean Isotropic B | ||||
| X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 2OJV | 2.94 | 25 | 27191 | 25825 | 1366 | 94.99 | 0.24187 | 0.20069 | 0.19744 | 0.23171 | RANDOM | 19.774 | ||||
| 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] | |
| 0.5 | 1.39 | -0.36 | -0.33 | 0.73 | -1.11 | |
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 35.837 |
| r_dihedral_angle_4_deg | 16.115 |
| r_dihedral_angle_3_deg | 14.614 |
| r_dihedral_angle_1_deg | 5.226 |
| r_scangle_it | 1.247 |
| r_angle_refined_deg | 1.093 |
| r_scbond_it | 0.664 |
| r_mcangle_it | 0.622 |
| r_symmetry_hbond_refined | 0.347 |
| r_mcbond_it | 0.346 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 9514 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 464 |
| Heterogen Atoms | 340 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| DENZO | data reduction |
| MOLREP | phasing |
| REFMAC | refinement |
| AUTOMAR | data reduction |
| SCALEPACK | data scaling |
