6I3J
Bilirubin oxidase from Myrothecium verrucaria in complex with ferricyanide
X-RAY DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 2XLL | |
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 3.1 | 291.15 | 14% (w/v) PEG 3350, 0.1 M succinic acid, protein concentration 25 mg/ml |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 3.25 | 62.1 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 134.382 | α = 90 |
| b = 203.846 | β = 90 |
| c = 226.744 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | F 2 2 2 |
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 | MARMOSAIC 225 mm CCD | 2011-11-25 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | BESSY BEAMLINE 14.1 | 0.91841 | BESSY | 14.1 |
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | 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 | 2.59 | 47.3 | 100 | 0.144 | 0.157 | 0.061 | 0.994 | 13.5 | 6.5 | 48305 | -3.7 | 30.7 | |||||||
| Highest Resolution Shell | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||
| 1 | 2.59 | 2.67 | 99.9 | 0.858 | 0.963 | 0.428 | 0.608 | 2 | 4.9 | ||||||||||
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 | 2XLL | 2.59 | 47.3 | 48305 | 2442 | 99.89 | 0.1618 | 0.1601 | 0.2257 | random selection | 36.142 | ||||||
| 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] | |
| -0.47 | -1.72 | 2.19 | ||||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 31.954 |
| r_dihedral_angle_4_deg | 19.554 |
| r_dihedral_angle_3_deg | 14.747 |
| r_dihedral_angle_1_deg | 7.627 |
| r_long_range_B_refined | 6.017 |
| r_long_range_B_other | 6.004 |
| r_scangle_other | 4.194 |
| r_mcangle_other | 3.421 |
| r_mcangle_it | 3.42 |
| r_scbond_it | 2.808 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 8476 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 547 |
| Heterogen Atoms | 357 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| XDS | data scaling |
| XDS | data reduction |
| MOLREP | phasing |
