4C1R
Bacteroides thetaiotaomicron VPI-5482 mannosyl-6-phosphatase Bt3783
X-RAY DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 3MPR | PDB ENTRY 3MPR |
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | 8 | BT3783 CRYSTALS WERE OBTAINED BY MIXING EQUAL VOLUMES OF PURIFIED, RECOMBINANT BT3783 PROTEIN AT A CONCENTRATION OF 11.25 MG PER ML WITH MOTHER LIQUOR SOLUTION CONSISTING OF 15% (W/V) POLYTHEYLENE GLYCOL 4,000, 5% MPD (V PER V), 3 MM D-MANNOSE, AND 200 MM MGCL2., pH 8.0 | ||
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.14 | 42 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 65.44 | α = 90 |
| b = 148.81 | β = 117.1 |
| c = 71.45 | 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 | MARRESEARCH MX-300HE | COLLIMATING MIRROR WITH TWO STRIPES (SI, RH AND PT) , TOROIDAL FOCUSING MIRROR (RH AND PT) | 2013-03-06 | M | SINGLE WAVELENGTH | |||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | CLSI BEAMLINE 08ID-1 | CLSI | 08ID-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 | 40 | 99.9 | 0.12 | 7.8 | 3.6 | 70728 | ||||||||||||
| 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 | 2.21 | 100 | 0.44 | 3.3 | 3.6 | |||||||||||||
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 | PDB ENTRY 3MPR | 2.1 | 39.15 | 67122 | 3572 | 99.87 | 0.1582 | 0.1557 | 0.20495 | RANDOM | 22.277 | ||||||
| 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] | |
| -0.77 | -0.46 | 1.3 | -0.19 | |||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 37.509 |
| r_dihedral_angle_4_deg | 17.837 |
| r_dihedral_angle_3_deg | 15.265 |
| r_dihedral_angle_1_deg | 7.177 |
| r_scbond_it | 3.26 |
| r_mcangle_it | 3.062 |
| r_mcbond_it | 2.091 |
| r_angle_refined_deg | 1.529 |
| r_chiral_restr | 0.126 |
| r_bond_refined_d | 0.013 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 8627 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 820 |
| Heterogen Atoms | 8 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| AutoProcess | data reduction |
| SCALA | data scaling |
| PHASER | phasing |
