2IL4
Crystal structure of At1g77540-Coenzyme A Complex
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
---|---|---|---|
Type | Source | Accession Code | Details |
experimental model | PDB | 1XMT | PDB entry 1XMT |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 277 | PROTEIN SOLUTION (10 MG/ML PROTEIN, 0.050 M SODIUM CHLORIDE, 0.003 M SODIUM AZIDE, 0.0003 M TCEP, 0.005 M MES PH 6.0) MIXED IN A 1:1 RATIO WITH THE WELL SOLUTION (29% PEG 5000, 0.10 M SODIUM CITRATE, 0.10 M PIPES PH 6.5). CRYSTALS SOAKED 16 HOURS IN WELL SOLUTION SUPPLEMENTED WITH 0.009 M acetyl-Coenzyme. Crystals cryo-protected with fomblin 2500, vapor diffusion, hanging drop, temperature 277K |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
2.24 | 45.08 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 27.905 | α = 90 |
b = 63.941 | β = 90.86 |
c = 29.525 | γ = 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 | ADSC QUANTUM 315 | Double crystal monochromator, Si111, 2nd crystal sagital focus followed by Rh coated bent cylinder vertically focusing mirror | 2005-11-30 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 8-BM | 0.97949 | APS | 8-BM |
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 | 2.05 | 31.98 | 99.2 | 0.052 | 18.303 | 4.3 | 6473 |
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 | 2.05 | 2.1 | 98 | 0.251 | 4.993 | 3.9 | 432 |
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 | PDB entry 1XMT | 2.054 | 31.976 | 6458 | 636 | 99.095 | 0.166 | 0.16 | 0.22 | RANDOM | 33.963 |
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] | |
0.716 | 2.045 | -0.701 | 0.046 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 28.241 |
r_dihedral_angle_4_deg | 16.802 |
r_dihedral_angle_3_deg | 16.084 |
r_scangle_it | 6.514 |
r_dihedral_angle_1_deg | 5.958 |
r_scbond_it | 4.882 |
r_mcangle_it | 2.621 |
r_angle_refined_deg | 1.664 |
r_mcbond_it | 1.608 |
r_nbtor_refined | 0.305 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 728 |
Nucleic Acid Atoms | |
Solvent Atoms | 61 |
Heterogen Atoms | 48 |
Software
Software | |
---|---|
Software Name | Purpose |
DENZO | data reduction |
SCALEPACK | data scaling |
MOLREP | phasing |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
HKL-2000 | data reduction |