3BD6
Glycogen Phosphorylase complex with 1(-D-ribofuranosyl) cyanuric acid
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
---|---|---|---|
Type | Source | Accession Code | Details |
experimental model | PDB | 2PRJ | PDB ENTRY 2PRJ |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | SMALL TUBES | 6.7 | 289 | 10mM Bes buffer, 3mM DDT, pH6.7, SMALL TUBES, temperature 289K |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
2.47 | 50.16 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 128.62 | α = 90 |
b = 128.62 | β = 90 |
c = 116.379 | γ = 90 |
Symmetry | |
---|---|
Space Group | P 43 21 2 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 298 | CCD | MAR CCD 165 mm | 2005-10-02 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | EMBL/DESY, HAMBURG BEAMLINE X11 | 0.81 | EMBL/DESY, HAMBURG | X11 |
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 | 2 | 30 | 98.5 | 0.047 | 18.6 | 4.9 | 65282 | 65282 | -3 |
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) | |||||||||||
2 | 2.03 | 98.1 | 0.435 | 4.5 | 4.9 |
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 | FOURIER SYNTHESIS | THROUGHOUT | PDB ENTRY 2PRJ | 2 | 21.58 | 61937 | 3311 | 98.48 | 0.19092 | 0.19015 | 0.20515 | RANDOM | 34.177 |
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] | |
0.85 | 0.85 | -1.7 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 33.959 |
r_dihedral_angle_4_deg | 17.531 |
r_dihedral_angle_3_deg | 15.174 |
r_dihedral_angle_1_deg | 5.025 |
r_scangle_it | 1.969 |
r_scbond_it | 1.205 |
r_angle_refined_deg | 1.023 |
r_mcangle_it | 0.941 |
r_mcbond_it | 0.547 |
r_nbtor_refined | 0.302 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 6638 |
Nucleic Acid Atoms | |
Solvent Atoms | 263 |
Heterogen Atoms | 18 |
Software
Software | |
---|---|
Software Name | Purpose |
REFMAC | refinement |
ADSC | data collection |
DENZO | data reduction |
SCALEPACK | data scaling |