1VMF
CRYSTAL STRUCTURE OF a YBJQ-LIKE FOLD PROTEIN OF UNKNOWN FUNCTION (BH3498) FROM BACILLUS HALODURANS AT 1.46 A RESOLUTION
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, SITTING DROP, NANODROP | 7.5 | 277 | 8.0% Ethylene Glycol, 10.0% PEG 8000, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K |
| 2 | VAPOR DIFFUSION, SITTING DROP, NANODROP | 7.5 | 277 | 0.2M NaCl, 30.0% PEG 400, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.31 | 46.64 |
| 2.2 | 43.54 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 57.601 | α = 90 |
| b = 58.951 | β = 90 |
| c = 134.964 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | P 21 21 21 |
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 | ADSC QUANTUM 315 | flat mirror | 2004-06-11 | M | MAD | |||||
| 2 | 1 | x-ray | 100 | CCD | ADSC | 2004-08-27 | M | MAD | ||||||
| 1,2 | 1 | |||||||||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | ALS BEAMLINE 8.3.1 | ALS | 8.3.1 | |
| 2 | SYNCHROTRON | SSRL BEAMLINE BL11-1 | 0.97957,0.979694,1.019859 | SSRL | BL11-1 |
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 | 1.46 | 29.48 | 97.9 | 0.059 | 16.5 | 5.6 | 78750 | 28.11 | |||||||||||
| 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 | 1.46 | 1.54 | 92 | 0.742 | 2.4 | 3.7 | 10604 | ||||||||||||
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 | R-Free | R-Free Selection Details | Mean Isotropic B | |||||||
| X-RAY DIFFRACTION | MAD | THROUGHOUT | 1.46 | 29.48 | 74793 | 3955 | 97.69 | 0.14964 | 0.14832 | 0.17483 | RANDOM | 19.183 | |||||||
| 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] | |
| 0.6 | -0.04 | -0.56 | ||||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 31.922 |
| r_dihedral_angle_3_deg | 12.275 |
| r_dihedral_angle_4_deg | 10.902 |
| r_scangle_it | 6.223 |
| r_dihedral_angle_1_deg | 5.902 |
| r_scbond_it | 3.95 |
| r_mcangle_it | 2.692 |
| r_mcbond_it | 1.608 |
| r_angle_refined_deg | 1.368 |
| r_angle_other_deg | 0.826 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 3225 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 417 |
| Heterogen Atoms | 36 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| XDS | data scaling |
| SCALA | data scaling |
| SHELX | model building |
| SHARP | phasing |
| REFMAC | refinement |
| XDS | data reduction |
| CCP4 | data scaling |
| SHELX | phasing |
