3MZ2
Crystal structure of a Glycerophosphoryl diester phosphodiesterase (BDI_3922) from Parabacteroides distasonis ATCC 8503 at 1.55 A resolution
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 4 | 293 | 27.0000% polyethylene glycol 4000, 0.3000M ammonium sulfate, 0.1M sodium acetate pH 4.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.01 | 38.77 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 53.577 | α = 90 |
b = 90.481 | β = 111.95 |
c = 60.373 | γ = 90 |
Symmetry | |
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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 325 mm CCD | Flat mirror (vertical focusing) | 2009-12-03 | M | MAD |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SSRL BEAMLINE BL11-1 | 0.91837,0.97925,0.97895 | SSRL | BL11-1 |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Sym 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 | 1.55 | 47.615 | 100 | 0.08 | 8.7 | 3.8 | 77355 | 14.681 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1.55 | 1.63 | 100 | 0.61 | 0.61 | 2.3 | 3.7 | 11285 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | 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 | MAD | THROUGHOUT | 1.55 | 47.615 | 77315 | 3882 | 99.98 | 0.167 | 0.166 | 0.197 | RANDOM | 19.3 |
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] | |
0.15 | -0.34 | -0.95 | 0.54 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 33.904 |
r_dihedral_angle_4_deg | 14.262 |
r_dihedral_angle_3_deg | 13.113 |
r_dihedral_angle_1_deg | 6.129 |
r_scangle_it | 4.029 |
r_scbond_it | 2.535 |
r_angle_refined_deg | 1.592 |
r_mcangle_it | 1.402 |
r_angle_other_deg | 0.938 |
r_mcbond_it | 0.824 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4532 |
Nucleic Acid Atoms | |
Solvent Atoms | 529 |
Heterogen Atoms | 141 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
PHENIX | refinement |
MolProbity | model building |
SCALA | data scaling |
PDB_EXTRACT | data extraction |
MOSFLM | data reduction |
PHENIX | phasing |
SOLVE | phasing |