1ZTV
Crystal structure of a duf72 family protein (ef0366) from enterococcus faecalis v583 at 3.10 A resolution
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1VPY | pdb entry 1vpy |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP, NANODROP | 6.5 | 277 | 1.0M NaCitrate, 0.1M Cacodylate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
4.08 | 69.59 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 91.819 | α = 90 |
b = 92.358 | β = 90 |
c = 119.347 | 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 | ADSC QUANTUM 315 | Flat mirror (vertical focusing), single crystal Si(111) bent monochromator (horizontal focusing) | 2004-07-06 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SSRL BEAMLINE BL11-1 | SSRL | BL11-1 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (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 | 3.1 | 119.52 | 99.4 | 0.08 | 0.08 | 8.6 | 3.4 | 18876 |
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 | 3.1 | 3.27 | 99.7 | 0.392 | 0.392 | 1.9 | 3.5 |
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 (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||
X-RAY DIFFRACTION | MR | THROUGHOUT | pdb entry 1vpy | 3.1 | 73.13 | 17862 | 975 | 100 | 0.193 | 0.19257 | 0.191 | 0.224 | RANDOM | 77.153 |
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] | |
-0.99 | -1.31 | 2.3 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 31.674 |
r_dihedral_angle_3_deg | 11.289 |
r_dihedral_angle_4_deg | 9.97 |
r_dihedral_angle_1_deg | 4.42 |
r_scangle_it | 3.46 |
r_scbond_it | 2.268 |
r_mcangle_it | 1.376 |
r_mcbond_it | 0.809 |
r_angle_refined_deg | 0.647 |
r_angle_other_deg | 0.539 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4419 |
Nucleic Acid Atoms | |
Solvent Atoms | 12 |
Heterogen Atoms | 2 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
SCALA | data scaling |
MOSFLM | data reduction |
CCP4 | data scaling |
PHASER | phasing |