4IXX
Crystal structure of S213G variant DAH7PS without Tyr bound 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 | 4HSO | PDB ENTRY 4HSO |
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, temperature 293.15K, VAPOR DIFFUSION, HANGING DROP |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.33 | 47.31 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 73.064 | α = 90 |
b = 132.432 | β = 95.72 |
c = 75.028 | 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 210r | 2011-07-13 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | AUSTRALIAN SYNCHROTRON BEAMLINE MX1 | 0.9537 | Australian Synchrotron | MX1 |
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 | 1.931 | 74.654 | 99.4 | 0.067 | 15.3 | 3.8 | 55141 | 55141 |
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 | 2.4 | 2.47 | 99.9 | 0.486 | 2.7 | 3.8 | 4518 |
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 4HSO | 2.4 | 19.59 | 55115 | 3384 | 99.25 | 0.1935 | 0.1914 | 0.2247 | RANDOM | 48.9273 |
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] | |
-1.57 | -0.05 | 2.18 | -0.59 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 34.116 |
r_dihedral_angle_4_deg | 17.425 |
r_dihedral_angle_3_deg | 15.357 |
r_dihedral_angle_1_deg | 4.962 |
r_mcangle_it | 2.248 |
r_angle_refined_deg | 1.444 |
r_mcbond_it | 1.397 |
r_mcbond_other | 1.395 |
r_angle_other_deg | 1.24 |
r_chiral_restr | 0.079 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 10404 |
Nucleic Acid Atoms | |
Solvent Atoms | 100 |
Heterogen Atoms | 39 |
Software
Software | |
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Software Name | Purpose |
Aimless | data scaling |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
ADSC | data collection |
XSCALE | data scaling |