4ZGG
Crystal structure of a DJ-1 (PARK7) from Homo sapiens at 1.23 A resolution
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 8 | 277 | 5.00% polyethylene glycol 6000, 0.1M TRIS pH 8.0 |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
3.01 | 59.13 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 75.002 | α = 90 |
b = 75.002 | β = 90 |
c = 74.897 | γ = 120 |
Symmetry | |
---|---|
Space Group | P 31 2 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 | MARMOSAIC 325 mm CCD | Vertical focusing mirror; double crystal Si(111) monochromator | 2014-12-06 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SSRL BEAMLINE BL14-1 | SSRL | BL14-1 |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Sym I (Observed) | Rrim I (All) | Rpim I (All) | 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 | 1.23 | 29.796 | 98.3 | 0.115 | 0.124 | 0.046 | 8.1 | 6.9 | 69760 | 69760 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Rrim I (All) | Rpim I (All) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||
1 | 1.23 | 1.26 | 86.1 | 0.804 | 0.804 | 0.913 | 0.422 | 0.9 | 4.1 | 4473 |
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 | 1.23 | 29.796 | 69700 | 3374 | 98.23 | 0.1172 | 0.1164 | 0.1339 | RANDOM | 17.4434 |
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] | |
0.2 | 0.1 | 0.2 | -0.64 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 36.157 |
r_sphericity_free | 30.129 |
r_dihedral_angle_4_deg | 19.353 |
r_dihedral_angle_3_deg | 11.474 |
r_sphericity_bonded | 8.773 |
r_dihedral_angle_1_deg | 6.157 |
r_rigid_bond_restr | 2.717 |
r_mcbond_it | 2.064 |
r_mcangle_it | 2.034 |
r_mcbond_other | 1.992 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 1396 |
Nucleic Acid Atoms | |
Solvent Atoms | 198 |
Heterogen Atoms | 40 |
Software
Software | |
---|---|
Software Name | Purpose |
PDB_EXTRACT | data extraction |
SOLVE | phasing |
SCALA | data scaling |
REFMAC | refinement |
MOSFLM | data reduction |