1XX1
Structural basis for ion-coordination and the catalytic mechanism of sphingomyelinases D
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 5.5 | 293 | sulfate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
2.6 | 51.6 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 139.818 | α = 90 |
b = 139.818 | β = 90 |
c = 113.461 | γ = 120 |
Symmetry | |
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Space Group | P 65 |
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 | 2004-08-09 | M | SINGLE WAVELENGTH | ||||||
2 | 1 | 100 | IMAGE PLATE | MARRESEARCH | osmic mirrors | 2004-08-20 |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | LNLS BEAMLINE D03B-MX1 | 1.427 | LNLS | D03B-MX1 |
2 | ROTATING ANODE | OTHER |
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 | 1.75 | 30 | 99.5 | 0.057 | 22 | 20.5 | 125875 |
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) | |||||||||||
1.75 | 1.79 | 99.5 | 0.305 | 3.4 | 6.5 |
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 (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | SIRAS | THROUGHOUT | 1.75 | 30 | 119510 | 6315 | 99.51 | 0.198 | 0.18761 | 0.18566 | 0.22465 | RANDOM | 24.248 |
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] | |
0.04 | 0.02 | 0.04 | -0.05 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 36.728 |
r_dihedral_angle_3_deg | 14.564 |
r_dihedral_angle_4_deg | 14.26 |
r_dihedral_angle_1_deg | 6.53 |
r_scangle_it | 3.37 |
r_scbond_it | 2.308 |
r_mcangle_it | 1.634 |
r_angle_refined_deg | 1.551 |
r_mcbond_it | 0.955 |
r_nbtor_refined | 0.328 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 9076 |
Nucleic Acid Atoms | |
Solvent Atoms | 1018 |
Heterogen Atoms | 164 |
Software
Software | |
---|---|
Software Name | Purpose |
REFMAC | refinement |
MAR345 | data collection |
SCALEPACK | data scaling |
SHELXS | phasing |