4NLM
1.18 Angstrom resolution crystal structure of uncharacterized protein lmo1340 from Listeria monocytogenes EGD-e
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 5 | 295 | protein - 7.5 mg/mL in 10 mM Tris-HCl, pH 8.3, 0.5 M NaCl 5 mM BME, Crystallization - The PACT Suite (#D2: 0.1 M MMT buffer pH 5, 25 % (w/v) PEG1500, VAPOR DIFFUSION, SITTING DROP, temperature 295K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.15 | 42.74 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 49.224 | α = 90 |
b = 69.99 | β = 95.61 |
c = 52.905 | 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 | MARMOSAIC 225 mm CCD | Be lenses | 2012-08-21 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 21-ID-F | 0.97872 | APS | 21-ID-F |
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 | 1.18 | 30 | 95.9 | 0.076 | 31.7 | 3.6 | 112400 | 112400 | -3 | 12.3 |
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 | 1.18 | 1.2 | 97.4 | 0.459 | 2.33 | 2.9 | 5714 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Number Reflections (All) | 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 | THROUGHOUT | 1.18 | 24.21 | 106618 | 106618 | 5628 | 95.86 | 0.14678 | 0.14503 | 0.18116 | RANDOM | 19.499 |
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] | |
0.41 | -0.02 | 2.4 | -2.76 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_sphericity_free | 37.178 |
r_dihedral_angle_2_deg | 32.285 |
r_sphericity_bonded | 15.36 |
r_rigid_bond_restr | 12.872 |
r_dihedral_angle_3_deg | 9.117 |
r_dihedral_angle_4_deg | 6.941 |
r_dihedral_angle_1_deg | 4.886 |
r_angle_refined_deg | 1.594 |
r_angle_other_deg | 0.718 |
r_chiral_restr | 0.096 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2670 |
Nucleic Acid Atoms | |
Solvent Atoms | 499 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
Blu-Ice | data collection |
MLPHARE | phasing |
REFMAC | refinement |
HKL-3000 | data reduction |
HKL-3000 | data scaling |