2IMD
Structure of SeMet 2-hydroxychromene-2-carboxylate isomerase (HCCA isomerase)
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | microbatch under oil | 6.1 | 294 | crystallization solution: 1.2M sodium dihydrogen phosphate, 0.8M potassium hydrogen phosphate,0.2M lithium sulfate, 0.1M CAPS pH 6.1. Protein and crystallization solutions were mixed 1:1., microbatch under oil, temperature 294K |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.23 | 44.75 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 71.336 | α = 90 |
| b = 76.051 | β = 90 |
| c = 38.366 | 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 | 100 | IMAGE PLATE | RIGAKU RAXIS IV++ | BLUE MAX-FLUX CONFOCAL | 2004-07-07 | M | SINGLE WAVELENGTH | |||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | ROTATING ANODE | RIGAKU | 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 | 1.5 | 27 | 99.4 | 0.044 | 3.83 | 34098 | 34098 | ||||||||||||
| 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 | 1.5 | 1.55 | 0.291 | 2.2 | 2.27 | 6066 | |||||||||||||
Refinement
| Statistics | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work (Depositor) | R-Free (Depositor) | R-Free Selection Details | Mean Isotropic B | |||||||
| X-RAY DIFFRACTION | SAD plus SIR | THROUGHOUT | 1.6 | 20 | 26752 | 1488 | 99.94 | 0.18887 | 0.18679 | 0.22562 | RANDOM | 22.331 | |||||||
| Temperature Factor Modeling | ||||||
|---|---|---|---|---|---|---|
| Anisotropic B[1][1] | Anisotropic B[2][2] | Anisotropic B[3][3] | ||||
| -0.95 | -0.79 | 1.74 | ||||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 36.554 |
| r_dihedral_angle_4_deg | 20.274 |
| r_dihedral_angle_3_deg | 14.693 |
| r_dihedral_angle_1_deg | 4.751 |
| r_scangle_it | 4.035 |
| r_scbond_it | 2.694 |
| r_angle_refined_deg | 1.901 |
| r_mcangle_it | 1.846 |
| r_mcbond_it | 1.237 |
| r_nbtor_refined | 0.318 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 1630 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 215 |
| Heterogen Atoms | 72 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| CrystalClear | data collection |
| d*TREK | data reduction |
| d*TREK | data scaling |
| SOLVE | phasing |
