2C1G
Structure of Streptococcus pneumoniae peptidoglycan deacetylase (SpPgdA)
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | PROTEIN WAS CRYSTALLIZED FROM 35% PEG 200, 5% PEG 3000, 100 MM MES, PH 6; THEN SOAKED IN 10 MM ZNCL2. |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
2.2 | 43.8 |
Crystal Data
Unit Cell | |
---|---|
Length ( ? ) | Angle ( ? ) |
a = 55.529 | ¦Á = 90 |
b = 78.439 | ¦Â = 90 |
c = 99.515 | ¦Ã = 90 |
Symmetry | |
---|---|
Space Group | P 21 21 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 | CCD | MARRESEARCH | MIRROR | 2004-06-12 | M | MAD |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE BM14 | ESRF | BM14 |
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 | 15 | 99 | 0.05 | 15.1 | 3.5 | 44323 | 2 | 20.1 |
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 | 1.75 | 1.81 | 98 | 0.46 | 2.8 | 3.4 |
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 | 1.75 | 14.96 | 44041 | 906 | 99 | 0.211 | 0.211 | 0.242 | RANDOM | 30.1 |
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] | |
1.04 | 0.16 | -1.19 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
c_dihedral_angle_d | 23.5 |
c_scangle_it | 4.08 |
c_scbond_it | 2.77 |
c_mcangle_it | 2.68 |
c_mcbond_it | 1.81 |
c_angle_deg | 1.5 |
c_improper_angle_d | 0.93 |
c_bond_d | 0.009 |
c_bond_d_na | |
c_bond_d_prot |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 3098 |
Nucleic Acid Atoms | |
Solvent Atoms | 177 |
Heterogen Atoms | 14 |
Software
Software | |
---|---|
Software Name | Purpose |
CNS | refinement |
HKL | data reduction |
HKL | data scaling |
SHELX | phasing |