2XR7
Crystal Structure of Nicotiana tabacum malonyltransferase (NtMat1) complexed with malonyl-coa
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | 0.3M AMMONIUM ACETATE, 7% PEG 8K, 10% MPD, PH 5.5 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.5 | 64 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 98.079 | ¦Á = 90 |
b = 98.079 | ¦Â = 90 |
c = 151.84 | ¦Ã = 90 |
Symmetry | |
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Space Group | P 42 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 | 100 | CCD | ADSC QUANTUM 315 | M | SINGLE WAVELENGTH | |||||||
2 | 1 | x-ray | 100 | CCD | SX-165 | 2005-10-25 | M |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | NSLS BEAMLINE X29A | NSLS | X29A | |
2 | SYNCHROTRON | NSLS BEAMLINE X3A | NSLS | X3A |
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 | 3.1 | 20 | 99.4 | 0.11 | 20 | 4 | 25628 | 2 |
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 | 3.1 | 3.21 | 95.4 | 0.6 | 1.7 | 2.9 |
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 | SAD | THROUGHOUT | NONE | 3.1 | 20 | 12928 | 1001 | 99.6 | 0.23 | 0.226 | 0.289 | RANDOM | 82.65 |
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] | |
0.68 | 0.68 | -1.36 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.572 |
r_dihedral_angle_4_deg | 20.852 |
r_dihedral_angle_3_deg | 20.305 |
r_dihedral_angle_1_deg | 7.765 |
r_scangle_it | 3.991 |
r_scbond_it | 2.358 |
r_angle_refined_deg | 1.503 |
r_mcangle_it | 0.815 |
r_mcbond_it | 0.37 |
r_chiral_restr | 0.107 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 3544 |
Nucleic Acid Atoms | |
Solvent Atoms | |
Heterogen Atoms | 30 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
HKL-2000 | data reduction |
SCALEPACK | data scaling |
Auto-Rickshaw | phasing |