3UWB
Crystal structure of a probable peptide deformylase from strucynechococcus phage S-SSM7 in complex with actinonin
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3UWA |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7.3 | 290 | 60.8% MPD, 100MM NAHEPES PH 7.3- 7.4, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 290K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.43 | 49.49 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 47.81 | α = 90 |
b = 59.15 | β = 90 |
c = 61.46 | 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 | RIGAKU SATURN 944+ | 2011-08-16 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU MICROMAX-007 HF | 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 | 1.7 | 50 | 99.2 | 0.035 | 8.5 | 19769 | 19602 | -3 | 29.13 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 1.7 | 1.74 | 89.2 | 0.279 | 0.279 | 5.24 | 4.3 | 1417 |
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 | 3UWA | 1.7 | 42.62 | 19769 | 18627 | 977 | 0.156 | 0.156 | 0.155 | 0.171 | RANDOM | 20.36 |
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] | |
0.16 | -0.05 | -0.11 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 38.517 |
r_dihedral_angle_4_deg | 21.148 |
r_dihedral_angle_3_deg | 10.921 |
r_dihedral_angle_1_deg | 5.828 |
r_angle_refined_deg | 1.703 |
r_angle_other_deg | 0.993 |
r_chiral_restr | 0.115 |
r_bond_refined_d | 0.016 |
r_gen_planes_refined | 0.008 |
r_bond_other_d | 0.001 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1184 |
Nucleic Acid Atoms | |
Solvent Atoms | 202 |
Heterogen Atoms | 33 |
Software
Software | |
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Software Name | Purpose |
StructureStudio | data collection |
REFMAC | refinement |
XDS | data reduction |
XSCALE | data scaling |