4XDQ
Crystal structure of a Glycoside hydrolase family protein (Rv0315 ortholog) from Mycobacterium thermorestibile
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3RQ0 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7.5 | 289 | MythA.18623.a.B2.PS02026 at 20.8 mg/mL against JCSG+ screen condition G5, 5 mM CoCl2, 5 mM CdCl2, 5 mM MgCl2, 5 mM NiCl2, 0.1 M Hepes pH 7.5, 15% PEG 3350 supplemented with 20 % EG as cryo |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.22 | 44.61 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 74.55 | α = 90 |
b = 74.55 | β = 90 |
c = 95.53 | γ = 90 |
Symmetry | |
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Space Group | P 43 21 2 |
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 300 mm CCD | 2014-12-04 | 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) | 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 | 1.35 | 50 | 100 | 0.059 | 0.061 | 28.25 | 14.4 | 59755 | -3 | 18.076 |
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 | 1.35 | 1.39 | 100 | 0.532 | 0.552 | 5.4 | 14.3 |
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 | 3rq0 | 1.35 | 50 | 56708 | 2968 | 99.97 | 0.1264 | 0.1253 | 0.1479 | RANDOM | 14.451 |
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] | |
-0.56 | -0.56 | 1.11 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 33.355 |
r_dihedral_angle_4_deg | 24.391 |
r_dihedral_angle_3_deg | 9.765 |
r_dihedral_angle_1_deg | 7.272 |
r_sphericity_bonded | 5.883 |
r_rigid_bond_restr | 1.703 |
r_angle_refined_deg | 1.361 |
r_mcangle_it | 1.227 |
r_mcbond_it | 0.961 |
r_mcbond_other | 0.96 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1895 |
Nucleic Acid Atoms | |
Solvent Atoms | 340 |
Heterogen Atoms | 26 |
Software
Software | |
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Software Name | Purpose |
XDS | data reduction |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
XSCALE | data scaling |
BALBES | phasing |