7LBK
Crystal structure of human Survivin bound to histone H3 T3phK4me3 peptide
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 289 | The crystal was obtained by mixing 1 uL of protein at 10 mg/mL with 1 uL of mother liquor composed of 0.16 M potassium/sodium tartrate, 14% PEG 3350. |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
3.62 | 66.04 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 114.292 | α = 90 |
b = 71.369 | β = 129.33 |
c = 82.554 | γ = 90 |
Symmetry | |
---|---|
Space Group | C 1 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 | RAYONIX MX-300 | 2013-06-21 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 21-ID-D | 1.27822 | APS | 21-ID-D |
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 | 2.7 | 50 | 98.1 | 0.094 | 11.5 | 14.8 | 13890 |
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 | 2.7 | 2.75 | 93 | 0.756 | 11.4 |
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 | 2.7 | 41.04 | 11791 | 623 | 87.2 | 0.214 | 0.212 | 0.253 | RANDOM | 40.61 |
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] | |
-1.44 | -0.17 | 2.03 | -0.19 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 36.452 |
r_dihedral_angle_4_deg | 21.838 |
r_dihedral_angle_3_deg | 17.743 |
r_dihedral_angle_1_deg | 5.576 |
r_angle_refined_deg | 1.699 |
r_angle_other_deg | 1.051 |
r_chiral_restr | 0.083 |
r_bond_refined_d | 0.014 |
r_gen_planes_refined | 0.008 |
r_bond_other_d | 0.004 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 2250 |
Nucleic Acid Atoms | |
Solvent Atoms | 34 |
Heterogen Atoms | 2 |
Software
Software | |
---|---|
Software Name | Purpose |
REFMAC | refinement |
HKL-3000 | data scaling |
SCALEPACK | data scaling |
HKL-3000 | data reduction |
SHELXD | phasing |
DM | phasing |
MLPHARE | phasing |
HKL-3000 | phasing |
BUCCANEER | model building |
PDB_EXTRACT | data extraction |