3U28
Crystal structure of a Cbf5-Nop10-Gar1 complex from Saccharomyces cerevisiae
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
---|---|---|---|
Type | Source | Accession Code | Details |
experimental model | PDB | 2HVY |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 8.04 | 293 | 0.2M sodium malonate, 7%(w/v) polyethylene glycol 3350, pH 8.04, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
2.13 | 42.17 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 54.413 | α = 90 |
b = 59.386 | β = 90 |
c = 169.212 | γ = 90 |
Symmetry | |
---|---|
Space Group | P 21 21 21 |
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 | 2010-09-17 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | BSRF BEAMLINE 3W1A | 0.9796 | BSRF | 3W1A |
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 | 1.9 | 20 | 89.5 | 0.109 | 26.5 | 11.2 | 39859 |
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 | 1.9 | 1.93 | 78.8 | 0.432 | 4.2 | 10.2 |
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 | 2HVY | 1.9 | 19.92 | 37603 | 1971 | 89.7 | 0.20509 | 0.20355 | 0.23343 | RANDOM | 27.503 |
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] | |
-0.7 | 0.11 | 0.6 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 33.657 |
r_dihedral_angle_4_deg | 18.301 |
r_dihedral_angle_3_deg | 16.797 |
r_dihedral_angle_1_deg | 6.038 |
r_scangle_it | 3.352 |
r_scbond_it | 1.976 |
r_mcangle_it | 1.548 |
r_angle_refined_deg | 1.314 |
r_mcbond_it | 0.865 |
r_chiral_restr | 0.103 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 3749 |
Nucleic Acid Atoms | |
Solvent Atoms | 279 |
Heterogen Atoms |
Software
Software | |
---|---|
Software Name | Purpose |
PHASER | phasing |
REFMAC | refinement |
DENZO | data reduction |
SCALEPACK | data scaling |