4HSN
Crystal structure of DAH7PS from Neisseria meningitidis
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1OF8 | PDB ENTRY 1OF8 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 8.5 | 293.15 | A protein solution [11 mg/mL in 10 mM BTP buffer (pH 7.3)] was mixed 1:1 (v/v) with a reservoir solution containing 0.2 M trimethylamine N-oxide, 0.1 M Tris (pH 8.5), 15% 20% (w/v) PEG 2000 mme, 0.4 mM MnSO4. The drop sizes were 2 uL, and the volume of the reservoir solution was 500 uL, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.47 | 50.22 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 73.462 | α = 90 |
b = 137.279 | β = 96.42 |
c = 76.36 | 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 | ADSC QUANTUM 315r | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | AUSTRALIAN SYNCHROTRON BEAMLINE MX2 | 0.9537 | Australian Synchrotron | MX2 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 19.79 | 99.3 | 100515 | 100515 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||||
1 | 2 | 2.03 | 100 |
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 | MOLECULAR REPLACEMENT | THROUGHOUT | PDB ENTRY 1OF8 | 2 | 19.79 | 100477 | 6233 | 99.24 | 0.1774 | 0.1754 | 0.2085 | RANDOM | 37.0606 |
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] | |
-4.63 | -0.03 | 4.22 | 0.41 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 36.391 |
r_dihedral_angle_4_deg | 20.536 |
r_dihedral_angle_3_deg | 14.428 |
r_dihedral_angle_1_deg | 5.529 |
r_angle_refined_deg | 1.781 |
r_angle_other_deg | 1.478 |
r_chiral_restr | 0.113 |
r_bond_refined_d | 0.019 |
r_gen_planes_refined | 0.012 |
r_bond_other_d | 0.01 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 10432 |
Nucleic Acid Atoms | |
Solvent Atoms | 561 |
Heterogen Atoms | 64 |
Software
Software | |
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Software Name | Purpose |
PHASER | phasing |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
ADSC | data collection |
XSCALE | data scaling |
Aimless | data scaling |