2IHP
Yeast inorganic pyrophosphatase with magnesium and phosphate
X-RAY DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 1HUK | |
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION | 6 | 277 | 16% MPD, 10 mM MgCl2, 1 mM PO4-, pH 6.0, VAPOR DIFFUSION, temperature 277K |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.57 | 52.09 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 51.915 | α = 90 |
| b = 93.549 | β = 99.66 |
| c = 69.168 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | P 1 21 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 | MARRESEARCH | 2001-02-06 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | ESRF BEAMLINE BM1A | 0.8727 | ESRF | BM1A |
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (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 | 1.5 | 100 | 99.8 | 0.041 | 0.041 | 21.7 | 7.4 | 103964 | 103964 | ||||||||||
| Highest Resolution Shell | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
| 1.5 | 1.53 | 100 | 0.321 | 0.321 | 3.2 | 6946 | |||||||||||||
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-Work (DCC) | R-Free (Depositor) | R-Free (DCC) | R-Free Selection Details | Mean Isotropic B | ||
| X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 1HUK | 1.5 | 19.92 | 103685 | 103685 | 5172 | 99.75 | 0.163 | 0.163 | 0.162 | 0.16 | 0.18 | 0.18 | RANDOM | 14.071 | ||
| Temperature Factor Modeling | ||||||
|---|---|---|---|---|---|---|
| Anisotropic B[1][1] | Anisotropic B[1][3] | Anisotropic B[3][3] | ||||
| -0.01 | -0.01 | 0.01 | ||||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 39.669 |
| r_dihedral_angle_4_deg | 13.811 |
| r_dihedral_angle_3_deg | 11.602 |
| r_dihedral_angle_1_deg | 6.465 |
| r_scangle_it | 2.94 |
| r_scbond_it | 2.121 |
| r_angle_refined_deg | 1.445 |
| r_mcangle_it | 1.295 |
| r_mcbond_it | 0.935 |
| r_angle_other_deg | 0.792 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 4447 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 670 |
| Heterogen Atoms | 27 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| PDB_EXTRACT | data extraction |
| DENZO | data reduction |
| CCP4 | data scaling |
| MOLREP | phasing |
