3BOS
Crystal structure of a putative dna replication regulator HDA (SAMA_1916) from Shewanella amazonensis sb2b at 1.75 A resolution
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 6.9 | 277 | NANODROP, 0.2M Sodium thiocyanate, 20% PEG 3350, No Buffer pH 6.9, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.47 | 50.11 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 55.037 | ¦Á = 90 |
b = 64.032 | ¦Â = 90 |
c = 153.64 | ¦Ã = 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 325 mm CCD | Flat mirror (vertical focusing) | 2007-11-19 | M | MAD |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SSRL BEAMLINE BL11-1 | 0.97932, 0.91837 | SSRL | BL11-1 |
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 | 1.75 | 29.553 | 99.7 | 0.102 | 0.102 | 5.2 | 3.7 | 55436 | 19.79 |
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 | 1.75 | 1.8 | 100 | 0.643 | 0.643 | 1.2 | 3.7 | 4067 |
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 | MAD | THROUGHOUT | 1.75 | 29.553 | 55402 | 2813 | 99.54 | 0.168 | 0.166 | 0.201 | RANDOM | 16.815 |
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] | |
-0.12 | 0.74 | -0.62 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 32.638 |
r_dihedral_angle_4_deg | 15.132 |
r_dihedral_angle_3_deg | 12.442 |
r_scangle_it | 6.212 |
r_dihedral_angle_1_deg | 4.491 |
r_scbond_it | 4.456 |
r_mcangle_it | 2.551 |
r_mcbond_it | 1.585 |
r_angle_refined_deg | 1.474 |
r_angle_other_deg | 0.98 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3574 |
Nucleic Acid Atoms | |
Solvent Atoms | 554 |
Heterogen Atoms | 113 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
PHENIX | refinement |
SHELX | phasing |
MolProbity | model building |
SCALA | data scaling |
PDB_EXTRACT | data extraction |
MAR345 | data collection |
MOSFLM | data reduction |
SHELXD | phasing |
autoSHARP | phasing |