1Y5K
T-To-T(High) quaternary transitions in human hemoglobin: betaD99A deoxy low-salt (10 test sets)
X-RAY DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 1Y0W | PDB ENTRY 1Y0W |
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | batch | 7 | 298 | 10% PEG 6000, 10 mM potassium phosphate, 100 mM potassium chloride, 3 mM sodium dithionite, 10 mg/ml Hb, pH 7.0, batch, temperature 298K |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.59 | 52.48 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 97.46 | α = 90 |
| b = 99.88 | β = 90 |
| c = 66 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | P 21 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 | 277 | IMAGE PLATE | RIGAKU RAXIS IV | OSMIC MIRRORS | 2004-05-05 | 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 | 2.2 | 50 | 80.3 | 0.069 | 9.2 | 5.4 | 26819 | ||||||||||||
| 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) | |||||||||||
| 2.2 | 2.38 | 35.1 | 0.222 | 3.1 | 2.3 | 2292 | |||||||||||||
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 and local R-free | PDB ENTRY 1Y0W | 2.2 | 10 | 22469 | 2498 | 75.64 | 0.16783 | 0.16122 | 0.22655 | 10 SETS MATCHED to PDB ENTRY 1Y0W | 29 | ||||||
| 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] | |
| -0.43 | 2.53 | -2.1 | ||||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_3_deg | 19.082 |
| r_scangle_it | 4.422 |
| r_dihedral_angle_1_deg | 4.076 |
| r_scbond_it | 2.712 |
| r_angle_refined_deg | 2.056 |
| r_mcangle_it | 1.745 |
| r_angle_other_deg | 1.271 |
| r_mcbond_it | 0.936 |
| r_xyhbond_nbd_other | 0.27 |
| r_nbd_refined | 0.264 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 4380 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 175 |
| Heterogen Atoms | 172 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| CRYSTAL | data collection |
| MOSFLM | data reduction |
| SCALA | data scaling |
| X-PLOR | model building |
| REFMAC | refinement |
| CrystalClear | data reduction |
| CCP4 | data scaling |
| X-PLOR | phasing |
