2H99
Crystal structure of the effector binding domain of a BenM variant (R156H,T157S)
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2F97 | PDB accession code 2F97, BenM-EBD (high pH) |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | microbatch under oil | 288.2 | Precipitant: 0.015 M magnesium acetate, 0.05 M sodium cacodlylate, 1.7 M ammonium sulfate Protein: 20 mM tris HCl, 0.5 M NaCl, pH 7.9, 10% glycerol Equal volumes mixed, microbatch under oil. The growing crystallization solution was in pH 6 and the protein solution was in pH 7.9 condition, temperature 288.2K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.4 | 49.2 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 64.937 | α = 90 |
b = 66.506 | β = 90 |
c = 117.495 | 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 | MARRESEARCH | 2005-07-22 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 22-ID | 1.0000 | APS | 22-ID |
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 | 1.85 | 50 | 99.7 | 0.073 | 9.1 | 5.1 | 44035 |
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 | 1.85 | 1.92 | 99.3 | 99.3 | 0.484 | 4.8 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | 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 | MOLECULAR REPLACEMENT | THROUGHOUT | PDB accession code 2F97, BenM-EBD (high pH) | 1.85 | 44 | 43982 | 41766 | 2216 | 99.62 | 0.167 | 0.167 | 0.165 | 0.204 | RANDOM | 19.128 |
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] | |
1.75 | -0.49 | -1.26 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 36.318 |
r_dihedral_angle_3_deg | 11.159 |
r_dihedral_angle_4_deg | 9.713 |
r_dihedral_angle_1_deg | 5.735 |
r_scangle_it | 3.512 |
r_scbond_it | 2.654 |
r_mcangle_it | 1.306 |
r_angle_refined_deg | 1.085 |
r_mcbond_it | 0.917 |
r_angle_other_deg | 0.731 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3439 |
Nucleic Acid Atoms | |
Solvent Atoms | 578 |
Heterogen Atoms | 52 |
Software
Software | |
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Software Name | Purpose |
DENZO | data reduction |
SCALEPACK | data scaling |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
HKL-2000 | data scaling |
MOLREP | phasing |