4J07
Crystal structure of a PROBABLE RIBOFLAVIN SYNTHASE, BETA CHAIN RIBH (6,7-dimethyl-8-ribityllumazine synthase, DMRL synthase, Lumazine synthase) from Mycobacterium leprae
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1W19 | PDB ENTRY 1W19 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 8.5 | 290 | MD Morpheus screen C12: 12.5% PEG 1000, 12.5% PEG 3350, 12.5% MPD, 30mM sodium-nitrate, 30mM di-sodium hydrogen phosphate, 30mM ammonium sulfate, 100mM Bicine/Trizma base pH 8.5; MyleA.00730.a.A1.PS00659 at 20mg/ml; direct cryo, VAPOR DIFFUSION, SITTING DROP, temperature 290K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.71 | 55 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 109.95 | α = 90 |
b = 109.95 | β = 90 |
c = 288.33 | γ = 120 |
Symmetry | |
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Space Group | P 65 2 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 | RIGAKU SATURN 944+ | 2011-01-09 | 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) | 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 | 1.95 | 50 | 99.6 | 0.121 | 19.05 | 17.9 | 76305 | 75991 | -3 | 27.672 |
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 | 1.95 | 2 | 96.4 | 0.523 | 4.16 | 8.15 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB ENTRY 1W19 | 1.95 | 45.25 | 76305 | 71727 | 3829 | 99.6 | 0.2101 | 0.2101 | 0.2081 | 0.2461 | RANDOM | 22.737 |
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] | |
-0.05 | -0.05 | -0.05 | 0.15 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 34.971 |
r_dihedral_angle_4_deg | 14.554 |
r_dihedral_angle_3_deg | 13.141 |
r_dihedral_angle_1_deg | 5.597 |
r_angle_refined_deg | 1.521 |
r_mcangle_it | 1.502 |
r_mcbond_it | 0.939 |
r_mcbond_other | 0.938 |
r_angle_other_deg | 0.778 |
r_chiral_restr | 0.081 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 5354 |
Nucleic Acid Atoms | |
Solvent Atoms | 467 |
Heterogen Atoms | 35 |
Software
Software | |
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Software Name | Purpose |
XSCALE | data scaling |
PHASER | phasing |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
StructureStudio | data collection |
XDS | data reduction |