3HJV
1.7 Angstrom resolution crystal structure of an acyl carrier protein S-malonyltransferase from Vibrio cholerae O1 biovar eltor str. N16961
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 11 | 295 | The home made "Pioneer" screen, condition 11, mixed at 1:1 v/v ratio with protein sample (16 mg/mL, 0.3 M NaCl and 0.5 mM TCEP, 10mM Hepes pH 7.5), VAPOR DIFFUSION, SITTING DROP, temperature 295K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
1.85 | 33.58 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 46.525 | α = 90 |
b = 87.789 | β = 90 |
c = 121.957 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 21 |
Diffraction
Diffraction Experiment | ||||||||||||||
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ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | CCD | MARMOSAIC 300 mm CCD | Be Lenses/Diamond Laue Mono | 2009-03-14 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 21-ID-G | 0.979 | APS | 21-ID-G |
Data Collection
Overall | |||||||||||||||||||
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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 | 1.7 | 50 | 98.9 | 0.081 | 26.27 | 4.2 | 105566 | 105566 | -3 |
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 | 1.7 | 1.76 | 92.8 | 0.498 | 2.48 | 2.8 | 9855 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Number Reflections (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||
X-RAY DIFFRACTION | SAD | THROUGHOUT | 1.7 | 43.48 | 52586 | 52586 | 2841 | 98.95 | 0.14764 | 0.14764 | 0.14521 | 0.19314 | RANDOM | 13.998 |
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] | |
-0.32 | 0.4 | -0.08 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 33.108 |
r_dihedral_angle_3_deg | 10.591 |
r_dihedral_angle_4_deg | 8.806 |
r_scangle_it | 3.694 |
r_dihedral_angle_1_deg | 3.605 |
r_scbond_it | 2.257 |
r_angle_refined_deg | 1.489 |
r_mcangle_it | 1.24 |
r_angle_other_deg | 0.933 |
r_mcbond_it | 0.68 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4558 |
Nucleic Acid Atoms | |
Solvent Atoms | 663 |
Heterogen Atoms | 191 |
Software
Software | |
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Software Name | Purpose |
Blu-Ice | data collection |
REFMAC | refinement |
HKL-2000 | data reduction |
XDS | data reduction |
HKL-2000 | data scaling |
XSCALE | data scaling |
SHELXCD | phasing |
SHELXD | phasing |
SHELXE | model building |
Bp3 | phasing |
SOLOMON | phasing |
ARP/wARP | model building |