3BFP
Crystal Structure of apo-PglD from Campylobacter jejuni
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 6.5 | 298 | 0.1 M Bis-tris pH 6.5, 0.15 M ammonium acetate, 26% (v/v) PEG400 or 0.1 M Bis-tris pH 6.5, 0.2M postassium acetate, 21% (v/v) PEG 400, vapor diffusion, sitting drop, temperature 20K, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.36 | 63.4 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 86.462 | α = 90 |
b = 86.462 | β = 90 |
c = 65.547 | γ = 120 |
Symmetry | |
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Space Group | P 63 |
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 | IMAGE PLATE | MAR scanner 345 mm plate | M | SINGLE WAVELENGTH | |||||||
2 | 1 | x-ray | 100 | CCD | ADSC QUANTUM 4 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU FR-D | |||
2 | SYNCHROTRON | NSLS BEAMLINE X8C | 1.1 | NSLS | X8C |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | ||||||||
1,2 | 1.75 | 50 | 96.3 | 0.048 | 19.5 | 3.9 | 28194 | 1 | 1 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1.75 | 1.81 | 99 | 0.488 | 3 | 3.1 | 2779 |
Refinement
Statistics | |||||||||||||||||||
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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 | 32.51 | 28118 | 1420 | 99.73 | 0.2 | 0.198 | 0.225 | RANDOM | 23.584 |
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] | |
-0.01 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 37.14 |
r_dihedral_angle_3_deg | 13.658 |
r_dihedral_angle_4_deg | 6.005 |
r_dihedral_angle_1_deg | 5.6 |
r_scangle_it | 3.704 |
r_scbond_it | 2.324 |
r_mcangle_it | 1.405 |
r_angle_refined_deg | 1.193 |
r_mcbond_it | 0.817 |
r_nbtor_refined | 0.309 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1423 |
Nucleic Acid Atoms | |
Solvent Atoms | 116 |
Heterogen Atoms | 13 |
Software
Software | |
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Software Name | Purpose |
DENZO | data reduction |
SCALEPACK | data scaling |
SHARP | phasing |
DM | phasing |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
HKL-2000 | data collection |