4XXP
Crystal Structure of an Uncharacterized Protein (Rv0315 ortholog) from Mycobacterium paratuberculosis
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 4PQ9 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 4.2 | 290 | JCSG+(c1): 20% PEG-8000, 100mM Sodium phosphate dibasic/ citric acid, pH=4.2, 200mM Sodium Chloride mixed with MypaA.18623.a.B2.PS01983 at 26.32 mg/ml, tray 252788c1258195b4 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
1.75 | 29.72 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 36.03 | α = 90 |
b = 49.53 | β = 95.21 |
c = 55.31 | 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 | RIGAKU SATURN 944+ | 2014-12-31 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU FR-E+ SUPERBRIGHT | 1.5418 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | 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 | 1.6 | 50 | 94.8 | 0.045 | 0.046 | 35.5 | 12 | 24420 | -3 | 10.02 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 1.6 | 1.64 | 83.5 | 0.21 | 0.225 | 8.04 | 7.4 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 4PQ9 | 1.6 | 36.83 | 1.35 | 24420 | 2068 | 94.83 | 0.1427 | 0.1401 | 0.1706 | 13.5548 |
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] | |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 12.408 |
f_angle_d | 1.157 |
f_chiral_restr | 0.057 |
f_bond_d | 0.008 |
f_plane_restr | 0.006 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1635 |
Nucleic Acid Atoms | |
Solvent Atoms | 259 |
Heterogen Atoms | 1 |
Software
Software | |
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Software Name | Purpose |
XSCALE | data scaling |
PHENIX | refinement |
PDB_EXTRACT | data extraction |
BALBES | phasing |