2H1J
3.1 A X-ray structure of putative Oligoendopeptidase F: Crystals grown by microfluidic seeding
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | 7 | 296 | PRECIPITATION FROM A HANGING DROP VAPOR DIFFUSION TRIAL (60% TASCIMATE IN BIS-TRIS PROPANE PH= 7.0) WAS USED TO SEED INTO A 45% TASCIMATE SOLUTION USING A MICROFLUIDIC MICROBATCH SEEDING TECHNIQUE. CONCENTRATION OF PROTEIN WAS 17 MG/ML., TEMPERATURE 296K , pH 7.00 | |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 3.83 | 67.87 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 119.324 | α = 90 |
| b = 119.324 | β = 90 |
| c = 248.736 | γ = 120 |
| Symmetry | |
|---|---|
| Space Group | P 31 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 | CCD | MARMOSAIC 300 mm CCD | ADJUSTABLE FOCUSING MIRRORS. K-B GEOMETRY | 2006-04-01 | M | SINGLE WAVELENGTH | |||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | APS BEAMLINE 23-ID-D | APS | 23-ID-D | |
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 | 3.1 | 50 | 99.9 | 0.097 | 9.28 | 3.4 | 37927 | ||||||||||||
| 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 | 3.1 | 3.21 | 100 | 0.392 | 1.88 | 3.4 | |||||||||||||
Refinement
| Statistics | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Number Reflections (All) | 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 | SAD | THROUGHOUT | 3.1 | 20 | 31069 | 35830 | 1892 | 99.96 | 0.18923 | 0.18735 | 0.22529 | RANDOM | 69.79 | ||||||
| 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] | |
| 0.86 | 0.43 | 0.86 | -1.29 | |||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 35.291 |
| r_dihedral_angle_3_deg | 20.015 |
| r_dihedral_angle_4_deg | 18.902 |
| r_dihedral_angle_1_deg | 5.213 |
| r_scangle_it | 1.133 |
| r_angle_refined_deg | 1.131 |
| r_scbond_it | 0.775 |
| r_mcangle_it | 0.439 |
| r_nbtor_refined | 0.324 |
| r_mcbond_it | 0.298 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 9337 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 2 |
| Heterogen Atoms | 2 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| HKL-2000 | data reduction |
| HKL-2000 | data scaling |
| SOLVE | phasing |
