5YRX
Crystal structure of a hypothetical protein Rv3716c from Mycobacterium tuberculosis
X-RAY DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 1YBX | |
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | BATCH MODE | 5.5 | 293 | 20mM Sodium phosphate pH 5.5 0.1M Cadmium chloride 0.1M Magnesium chloride 0.1M Nickel chloride 24% PEG 4000 |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.31 | 41.88 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 35.11 | α = 90 |
| b = 183.75 | β = 90 |
| c = 37.25 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | C 2 2 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 | IMAGE PLATE | MAR scanner 345 mm plate | 2017-07-02 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | ROTATING ANODE | RIGAKU | 1.54 | ||
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | R Sym I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | 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 | 37.25 | 99.9 | 0.08 | 0.031 | 0.086 | 0.025 | 0.997 | 24.6 | 13.7 | 9968 | 14.8 | |||||||
| Highest Resolution Shell | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||
| 1 | 1.9 | 1.94 | 100 | 0.227 | 0.239 | 0.244 | 0.091 | 0.985 | 12.1 | 13.5 | |||||||||
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 | 1YBX | 1.9 | 32 | 9467 | 464 | 99.63 | 0.17423 | 0.17215 | 0.21594 | RANDOM | 31.881 | ||||||
| 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] | |
| -0.31 | 1.57 | -1.27 | ||||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 32.71 |
| r_dihedral_angle_3_deg | 15.229 |
| r_dihedral_angle_4_deg | 14.011 |
| r_long_range_B_refined | 9.208 |
| r_long_range_B_other | 9.108 |
| r_dihedral_angle_1_deg | 8.188 |
| r_scangle_other | 7.057 |
| r_scbond_other | 4.906 |
| r_scbond_it | 4.902 |
| r_mcangle_other | 4.777 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 482 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 62 |
| Heterogen Atoms | 13 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| iMOSFLM | data reduction |
| SCALA | data scaling |
| PHASER | phasing |
