3MQ3
Crystal structure of native bovine PDP1c
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | Hanging drop | 7.5 | 298 | The protein solution was 20mg/mL in 10 mM Tris-HCl, pH 7.3, 50 mM NaCl, 1mM MnSO4, 2mM DTT, and 1mM benzamide. The well solution (mixed 1:1) contained 0.10M HEPES, pH 7.5 and 20% Jeffamine M-600., Hanging drop, temperature 298K |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.68 | 54.11 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 75.274 | α = 90 |
| b = 75.274 | β = 90 |
| c = 172.637 | γ = 120 |
| Symmetry | |
|---|---|
| Space Group | P 32 2 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 | IMAGE PLATE | RIGAKU RAXIS IV | 1999-12-02 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | ROTATING ANODE | RIGAKU RU200 | 1.5418 | ||
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 | 2.8 | 27 | 96.9 | 0.085 | 20.6 | 4.7 | 14135 | ||||||||||||
| 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 | 2.8 | 2.9 | 97.9 | 0.34 | 7.6 | 5 | |||||||||||||
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 | MOLECULAR REPLACEMENT | THROUGHOUT | PDB: | 2.8 | 27 | 13413 | 716 | 96.99 | 0.22706 | 0.22415 | 0.23 | 0.28433 | 0.28 | RANDOM | 42.471 | ||||
| Temperature Factor Modeling | ||||||
|---|---|---|---|---|---|---|
| Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[2][2] | Anisotropic B[3][3] | |||
| 0.6 | 0.3 | 0.6 | -0.9 | |||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 38.326 |
| r_dihedral_angle_4_deg | 20.781 |
| r_dihedral_angle_3_deg | 18.623 |
| r_dihedral_angle_1_deg | 7.782 |
| r_scangle_it | 3.701 |
| r_scbond_it | 2.478 |
| r_angle_refined_deg | 1.894 |
| r_mcangle_it | 1.832 |
| r_mcbond_it | 1.106 |
| r_nbtor_refined | 0.32 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 2967 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 99 |
| Heterogen Atoms | 2 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| PDB_EXTRACT | data extraction |
| CrystalClear | data collection |
| DENZO | data reduction |
| SCALEPACK | data scaling |
| HKL-2000 | data scaling |
| MOLREP | phasing |
