2CBI
Structure of the Clostridium perfringens NagJ family 84 glycoside hydrolase, a homologue of human O-GlcNAcase
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | 6.5 | 0.2 M AMMONIUM SULFATE, 0.1 M SODIUM CACODYLATE PH 6.5, 30 % PEG 8000) AND 0.25 MICROLITER OF 40 % V/V GAMMA-BUTYROLACTONE TO A 1 PLUS MICROLITER DROP |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
2.51 | 47.5 |
Crystal Data
Unit Cell | |
---|---|
Length ( ? ) | Angle ( ? ) |
a = 119.939 | ¦Á = 90 |
b = 147.38 | ¦Â = 90 |
c = 157.687 | ¦Ã = 90 |
Symmetry | |
---|---|
Space Group | I 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 | 157 | CCD | MARRESEARCH | MIRROR | 2005-10-31 | M | SINGLE WAVELENGTH |
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 | 2.25 | 20 | 100 | 0.11 | 7.7 | 25.4 | 65956 | 2 |
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 | 2.25 | 2.33 | 100 | 0.48 | 7.6 | 18.6 |
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 | SAD | THROUGHOUT | 2.25 | 20 | 65296 | 659 | 99.9 | 0.169 | 0.169 | 0.22 | RANDOM | 14.66 |
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] | |
0.92 | 1.62 | -2.54 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 40.218 |
r_dihedral_angle_4_deg | 20.703 |
r_dihedral_angle_3_deg | 16.27 |
r_dihedral_angle_1_deg | 6.373 |
r_scangle_it | 5.034 |
r_scbond_it | 3.436 |
r_mcangle_it | 1.954 |
r_angle_refined_deg | 1.47 |
r_mcbond_it | 1.266 |
r_nbtor_refined | 0.302 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 9240 |
Nucleic Acid Atoms | |
Solvent Atoms | 650 |
Heterogen Atoms | 41 |
Software
Software | |
---|---|
Software Name | Purpose |
REFMAC | refinement |
DENZO | data reduction |
SCALEPACK | data scaling |
SOLVE | phasing |