3LUZ
Crystal structure of extragenic suppressor protein suhB from Bartonella henselae, via combined iodide SAD molecular replacement
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2QFL |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7.5 | 289 | 24 mg/mL protein in 0.2 M MgCl2, 0.1 M Hepes pH 7.5, 30% PEG 400 soaked into 0.2 M MgCl2, 0.75 M KI, 0.1 M Hepes pH 8.2, 35% PEG 400; crystal tracking ID for growth 206523d2 and 206575a1 for iodide soak, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
1.94 | 36.72 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 48.54 | α = 90 |
b = 81.28 | β = 98.78 |
c = 58.76 | γ = 90 |
Symmetry | |
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Space Group | P 1 21 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 | RIGAKU SATURN 944+ | 2010-01-13 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU FR-E+ SUPERBRIGHT | 1.5418 |
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 | 2.05 | 30 | 96.7 | 0.066 | 18.26 | 7.3 | 27477 | -3 | 38.09 |
Highest Resolution Shell | |||||||||||||||||||
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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 | 2.05 | 2.1 | 82.1 | 0.439 | 4.2 | 5.9 |
Refinement
Statistics | |||||||||||||||||||
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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, MOLECULAR REPLACEMENT | THROUGHOUT | 2qfl | 2.05 | 29.04 | 27458 | 1395 | 96.76 | 0.219 | 0.217 | 0.262 | RANDOM | 57.542 |
Temperature Factor Modeling | ||||||
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Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
-0.77 | -0.27 | 2.65 | -1.97 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 36.204 |
r_dihedral_angle_3_deg | 16.803 |
r_dihedral_angle_4_deg | 16.274 |
r_dihedral_angle_1_deg | 6.379 |
r_angle_refined_deg | 1.472 |
r_chiral_restr | 0.091 |
r_bond_refined_d | 0.014 |
r_gen_planes_refined | 0.006 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3508 |
Nucleic Acid Atoms | |
Solvent Atoms | 124 |
Heterogen Atoms | 15 |
Software
Software | |
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Software Name | Purpose |
XSCALE | data scaling |
PHASER | phasing |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
XDS | data reduction |