3U7Z
Crystal structure of a putative metal binding protein RUMGNA_00854 (ZP_02040092.1) from Ruminococcus gnavus ATCC 29149 at 1.30 A resolution
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2BB6 | PDB entry 2BB6 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7.9 | 293 | 34.0% polyethylene glycol 400, 0.20M calcium acetate, 0.1M HEPES pH 7.9, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
1.83 | 32.85 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 29.685 | α = 73.13 |
b = 30.474 | β = 83.79 |
c = 47.156 | γ = 89.3 |
Symmetry | |
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Space Group | P 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 | MARMOSAIC 325 mm CCD | double crystal monochromator | 2011-06-23 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SSRL BEAMLINE BL9-2 | SSRL | BL9-2 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Sym 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 | 1.3 | 29.504 | 95 | 0.067 | 7.9 | 2.5 | 36776 | 36776 |
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 | 1.3 | 1.33 | 92.2 | 0.589 | 0.589 | 1.2 | 2.5 | 2654 |
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 2BB6 | 1.3 | 29.504 | 36769 | 1824 | 95.03 | 0.1404 | 0.1379 | 0.1887 | RANDOM | 16.8017 |
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] | |
0.02 | 0.13 | -0.09 | 0.06 | -0.14 | 0.01 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 39.664 |
r_dihedral_angle_3_deg | 11.339 |
r_sphericity_free | 9.434 |
r_scangle_it | 6.877 |
r_dihedral_angle_1_deg | 5.936 |
r_scbond_it | 4.807 |
r_sphericity_bonded | 4.225 |
r_mcangle_it | 3.902 |
r_mcbond_it | 2.731 |
r_rigid_bond_restr | 2.177 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1504 |
Nucleic Acid Atoms | |
Solvent Atoms | 167 |
Heterogen Atoms | 44 |
Software
Software | |
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Software Name | Purpose |
MolProbity | model building |
PDB_EXTRACT | data extraction |
MOLREP | phasing |
SCALA | data scaling |
REFMAC | refinement |
MOSFLM | data reduction |