2IF7
Crystal Structure of NTB-A
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7.4 | 277 | 0.4-0.5 M CaCl2, 0.1 M HEPES pH 7.4, 1.0 mM Pt(NH3)2Cl2, 4% PEG-400, Vapor diffusion, Sitting drop, temperature 277K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
4.13 | 70.25 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 121.196 | α = 90 |
b = 148.452 | β = 112.86 |
c = 86.572 | γ = 90 |
Symmetry | |
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Space Group | C 1 2 1 |
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 | ADSC QUANTUM 315 | 2005-10-20 | M | MAD | ||||||
2 | 1 | |||||||||||||
3 | 1 |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | NSLS BEAMLINE X29A | 0.9789,0.9791,0.9714 | NSLS | X29A |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | R Sym 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 | 40 | 99.7 | 0.059 | 0.048 | 15.1 | 3.2 | 28402 | 28402 | 51 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 3 | 3.11 | 99.9 | 0.348 | 0.303 | 3.08 | 3.2 | 2838 |
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 | MAD | THROUGHOUT | 3 | 40 | 28151 | 28151 | 1413 | 99.67 | 0.216 | 0.216 | 0.213 | 0.266 | RANDOM | 83.603 |
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] | |
2.85 | 3.14 | -1.44 | 1.02 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.35 |
r_dihedral_angle_3_deg | 19.258 |
r_dihedral_angle_4_deg | 15.413 |
r_dihedral_angle_1_deg | 6.209 |
r_scangle_it | 4.239 |
r_scbond_it | 2.517 |
r_mcangle_it | 1.793 |
r_angle_refined_deg | 1.085 |
r_mcbond_it | 1.004 |
r_nbtor_refined | 0.332 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 5960 |
Nucleic Acid Atoms | |
Solvent Atoms | 3 |
Heterogen Atoms | 3 |
Software
Software | |
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Software Name | Purpose |
DENZO | data reduction |
SCALEPACK | data scaling |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
CBASS | data collection |
HKL-2000 | data reduction |
SHELXD | phasing |
SHELXE | model building |
SOLVE | phasing |
RESOLVE | phasing |
Coot | model building |
O | model building |