2WVM
H309A mutant of Mannosyl-3-phosphoglycerate synthase from Thermus thermophilus HB27 in complex with GDP-alpha-D-Mannose and Mg(II)
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
---|---|---|---|
Type | Source | Accession Code | Details |
experimental model | PDB | 2WVL | PDB ENTRY 2WVL |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | 6.5 | 0.2 M MAGNESIUM ACETATE, 0.1 M SODIUM CACODYLATE PH 6.5, 30-35% MPD WITH 600 MM ZNCL2 AS AN ADDITIVE, 1-5 MM GDP-ALPHA-D-MANNOSE |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
3.6 | 65.7 |
Crystal Data
Unit Cell | |
---|---|
Length ( ? ) | Angle ( ? ) |
a = 112.766 | ¦Á = 90 |
b = 112.766 | ¦Â = 90 |
c = 199.69 | ¦Ã = 90 |
Symmetry | |
---|---|
Space Group | P 41 21 2 |
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 CCD | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I04 | Diamond | I04 |
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 | 2.977 | 48.9 | 94 | 0.04 | 15.4 | 2.7 | 25598 |
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 | 2.977 | 3.16 | 80.6 | 0.37 | 2.09 | 2.1 |
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 2WVL | 2.977 | 98.19 | 24263 | 1292 | 94.15 | 0.17643 | 0.17355 | 0.23163 | RANDOM | 55.868 |
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] | |
3.23 | 3.23 | -6.46 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 37.324 |
r_dihedral_angle_4_deg | 20.468 |
r_dihedral_angle_3_deg | 19.749 |
r_dihedral_angle_1_deg | 6.6 |
r_scangle_it | 4.622 |
r_scbond_it | 2.685 |
r_angle_refined_deg | 1.642 |
r_mcangle_it | 1.34 |
r_mcbond_it | 0.656 |
r_chiral_restr | 0.106 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 5880 |
Nucleic Acid Atoms | |
Solvent Atoms | 15 |
Heterogen Atoms | 83 |
Software
Software | |
---|---|
Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
XDS | data scaling |
PHASER | phasing |