4Q51
Crystal structure of a putative molybdenum cofactor biosynthesis protein F from Burkholderia cenocepacia J2315
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, SITTING DROP | 8.5 | 292 | 0.2 M Calcium Chloride, 0.1 M Tris-HCl, 25 % (w/v) PEG4000, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 292K |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 1.96 | 37.13 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 69.402 | α = 90 |
| b = 46.163 | β = 99.14 |
| c = 77.293 | 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 | CCD | MARMOSAIC 225 mm CCD | Beryllium Lenses | 2014-02-27 | M | SINGLE WAVELENGTH | |||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | APS BEAMLINE 21-ID-F | 0.97872 | APS | 21-ID-F |
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 | 1.9 | 30 | 96.7 | 0.08 | 24.8 | 6.6 | 37347 | 37347 | -3 | 27.3 | |||||||||
| 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 | 1.9 | 1.93 | 93.7 | 0.5 | 4.2 | 6 | |||||||||||||
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 | 1.9 | 29.57 | 35312 | 35312 | 1869 | 95.87 | 0.16274 | 0.16028 | 0.20871 | RANDOM | 21.182 | ||||||
| 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] | |
| -0.19 | 0.01 | 0.07 | 0.12 | |||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 35.17 |
| r_dihedral_angle_4_deg | 15.509 |
| r_dihedral_angle_3_deg | 13.449 |
| r_dihedral_angle_1_deg | 6.338 |
| r_long_range_B_refined | 6.009 |
| r_long_range_B_other | 5.801 |
| r_scangle_other | 3.391 |
| r_scbond_it | 2.139 |
| r_scbond_other | 2.138 |
| r_mcangle_it | 1.839 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 4113 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 474 |
| Heterogen Atoms | 2 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| Blu-Ice | data collection |
| PHENIX | model building |
| REFMAC | refinement |
| HKL-2000 | data reduction |
| HKL-2000 | data scaling |
| PHENIX | phasing |
