2Q8P
Crystal Structure of selenomethionine labelled S. aureus IsdE complexed with heme
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 5.5 | 294 | 50 mM MES, 0.2 M ammonuim acetate, 28% PEG 4000, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
2.42 | 49.19 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 63.527 | α = 90 |
b = 63.527 | β = 90 |
c = 144.247 | γ = 90 |
Symmetry | |
---|---|
Space Group | P 43 21 2 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 77 | CCD | MARMOSAIC 325 mm CCD | Flat mirror (vertical focusing), single crystal Si(111) bent monochromator (horizontal focusing) | 2007-02-19 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SSRL BEAMLINE BL11-1 | 0.978894 | SSRL | BL11-1 |
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 | 1.95 | 50 | 86 | 0.068 | 30 | 12.1 | 19425 |
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 | 1.95 | 2.02 | 79 | 0.359 | 7.6 |
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 | 1.95 | 50 | 17938 | 963 | 84.6 | 0.20422 | 0.20105 | 0.26293 | RANDOM | 32.785 |
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] | |
0.43 | 0.43 | -0.85 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 38.103 |
r_dihedral_angle_4_deg | 18.514 |
r_dihedral_angle_3_deg | 17.497 |
r_dihedral_angle_1_deg | 9.415 |
r_scangle_it | 2.772 |
r_scbond_it | 1.994 |
r_angle_refined_deg | 1.39 |
r_mcangle_it | 1.072 |
r_mcbond_it | 0.754 |
r_nbtor_refined | 0.303 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 2076 |
Nucleic Acid Atoms | |
Solvent Atoms | 183 |
Heterogen Atoms | 43 |
Software
Software | |
---|---|
Software Name | Purpose |
DENZO | data reduction |
SCALEPACK | data scaling |
SOLVE | phasing |
RESOLVE | phasing |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
HKL-2000 | data collection |
HKL-2000 | data reduction |