2NT0
Acid-beta-glucosidase low pH, glycerol bound
X-RAY DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 1OGS | 1OGS monomer |
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 4.5 | 298 | 1 M Ammonium Sulfate 0.17 M Guanidinium HCl 0.02 M KCl 0.1 M Acetate buffer pH 4.5 Cryoprotectant includes 20% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 3.17 | 61.24 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( ? ) | Angle ( ? ) |
| a = 107.941 | ¦Á = 90 |
| b = 91.759 | ¦Â = 110.96 |
| c = 152.81 | ¦Ã = 90 |
| Symmetry | |
|---|---|
| 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 | MARRESEARCH | 2005-09-30 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | APS BEAMLINE 23-ID-B | 1 | APS | 23-ID-B |
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 | 1.8 | 50 | 84.8 | 0.062 | 7.6 | 2.1 | 220956 | 24.35 | |||||||||||
| Highest Resolution Shell | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
| 1 | 1.8 | 1.86 | 71.8 | 0.417 | 1.5 | 1.8 | 18569 | ||||||||||||
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 | 1OGS monomer | 1.79 | 50 | 220955 | 11117 | 84.13 | 0.181 | 0.179 | 0.215 | RANDOM | 24.352 | ||||||
| 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] | |
| 2.15 | -0.33 | -1.24 | -1.15 | |||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 36.931 |
| r_dihedral_angle_4_deg | 18.413 |
| r_dihedral_angle_3_deg | 14.367 |
| r_dihedral_angle_1_deg | 6.833 |
| r_scangle_it | 3.622 |
| r_scbond_it | 2.485 |
| r_angle_refined_deg | 1.585 |
| r_mcangle_it | 1.53 |
| r_mcbond_it | 1.011 |
| r_nbtor_refined | 0.308 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 15720 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 1710 |
| Heterogen Atoms | 248 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| DENZO | data reduction |
| SCALEPACK | data scaling |
| REFMAC | refinement |
| PDB_EXTRACT | data extraction |
| MAR345 | data collection |
| HKL-2000 | data reduction |
