Crystal structure of the SeMet-labeled prolyl-4 hydroxylase (P4H) type I from green algae Chlamydomonas reinhardtii.
X-RAY DIFFRACTION
Crystallization
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 1.8 | 31.5 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 137.49 | α = 90 |
| b = 137.49 | β = 90 |
| c = 88.13 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | P 43 21 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 | MARRESEARCH | 2005-10-01 | M | MAD | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | EMBL/DESY, HAMBURG BEAMLINE BW7A | 0.9421, 0.9421, 0.9798 | EMBL/DESY, HAMBURG | BW7A |
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 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 | 1.93 | 25 | 99.1 | 0.06 | 11.8 | 3.8 | 457239 | 3 | |||||||||||
| 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 | 1.93 | 2.05 | 98.1 | 0.34 | 3.8 | ||||||||||||||
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 (Depositor) | R-Work (DCC) | R-Free (Depositor) | R-Free (DCC) | R-Free Selection Details | Mean Isotropic B | ||||
| X-RAY DIFFRACTION | MAD | THROUGHOUT | NONE | 1.93 | 19.87 | 60331 | 3176 | 99.6 | 0.192 | 0.188 | 0.1907 | 0.223 | 0.2239 | RANDOM | 26.74 | ||||
| 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] | |
| 0.26 | 0.26 | -0.52 | ||||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 30.912 |
| r_dihedral_angle_4_deg | 22.548 |
| r_dihedral_angle_3_deg | 14.122 |
| r_dihedral_angle_1_deg | 6.222 |
| r_scangle_it | 3.013 |
| r_scbond_it | 2.211 |
| r_angle_refined_deg | 1.526 |
| r_mcangle_it | 1.24 |
| r_mcbond_it | 0.875 |
| r_nbtor_refined | 0.296 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 5773 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 313 |
| Heterogen Atoms | 41 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| XDS | data reduction |
| XDS | data scaling |
| SOLVE | phasing |
