6M9R
Crystal structure of SznF from Streptomyces achromogenes var. streptozoticus NRRL 2697 with a bound N(delta)-hydroxy-N(omega)-methyl-L-arginine intermediate
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 6M9S | PDB entry 6M9S |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 8.5 | 298 | 0.1 M Tris, pH 8.5, 0.1 M magnesium chloride, 14-20% w/v PEG4000 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.19 | 43.94 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 57.95 | α = 90 |
b = 107.73 | β = 90 |
c = 150.54 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 21 |
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 | 2018-02-09 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 21-ID-G | 0.97856 | APS | 21-ID-G |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | CC (Half) | 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 | 1.685 | 54.09 | 99.9 | 0.084 | 0.089 | 0.998 | 14.01 | 8.2 | 107050 | 24 |
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) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||
1 | 1.69 | 1.79 | 99.9 | 0.877 | 0.935 | 0.825 | 2.52 | 8.2 |
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 6M9S | 1.69 | 54.08 | 100867 | 5310 | 99.98 | 0.17121 | 0.17018 | 0.19076 | RANDOM | 33.041 |
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] | |
0.11 | 0.79 | -0.9 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 31.016 |
r_dihedral_angle_4_deg | 17.628 |
r_dihedral_angle_3_deg | 12.427 |
r_dihedral_angle_1_deg | 5.051 |
r_long_range_B_refined | 4.736 |
r_long_range_B_other | 4.313 |
r_scangle_other | 1.445 |
r_angle_refined_deg | 1.172 |
r_mcangle_it | 0.931 |
r_mcangle_other | 0.931 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 7303 |
Nucleic Acid Atoms | |
Solvent Atoms | 979 |
Heterogen Atoms | 30 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
XSCALE | data scaling |
PHASER | phasing |