3A0I
Human glucokinase in complex with a synthetic activator
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
---|---|---|---|
Type | Source | Accession Code | Details |
experimental model | PDB | 1V4S | PDB ENTRY 1V4S |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6.6 | 298 | 30 % PEG 1500, HEPES, PH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
2.9 | 57.55 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 79.732 | α = 90 |
b = 79.732 | β = 90 |
c = 321.975 | γ = 120 |
Symmetry | |
---|---|
Space Group | P 65 2 2 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | DIFFRACTOMETER | WEISSENBERG | 2002-04-24 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | PHOTON FACTORY BEAMLINE BL-6B | 1.000 | Photon Factory | BL-6B |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (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 | 2.2 | 50 | 94.5 | 0.064 | 0.064 | 16.5 | 5 | 32108 | 30342 | 36.1 |
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) | |||||||||||
2.2 | 2.28 | 0.254 | 1.86 |
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 1V4S | 2.2 | 42.37 | 28759 | 1529 | 94.66 | 0.2285 | 0.22588 | 0.27702 | RANDOM | 35.812 |
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] | |
1.68 | 0.84 | 1.68 | -2.52 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 39.394 |
r_dihedral_angle_4_deg | 20.262 |
r_dihedral_angle_3_deg | 19.34 |
r_dihedral_angle_1_deg | 6.865 |
r_scangle_it | 5.673 |
r_scbond_it | 3.511 |
r_mcangle_it | 2.358 |
r_angle_refined_deg | 2.06 |
r_mcbond_it | 1.305 |
r_symmetry_vdw_refined | 0.449 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 3505 |
Nucleic Acid Atoms | |
Solvent Atoms | 137 |
Heterogen Atoms | 43 |
Software
Software | |
---|---|
Software Name | Purpose |
REFMAC | refinement |
WEIS | data scaling |
HKL-2000 | data reduction |
HKL-2000 | data scaling |