3BVD
Structure of Surface-engineered Cytochrome ba3 Oxidase from Thermus thermophilus under Xenon Pressure, 100psi 5min
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1XME | PDB ENTRY 1XME |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION | 7 | 297 | 6-9% PEG 2000, 50mM KCl, 7.5-30mM bis-Tris pH 7.0, 6.5mM nonyl-B-D-glucopyranoside , VAPOR DIFFUSION, temperature 297K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.21 | 61.65 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 119.726 | α = 90 |
b = 119.726 | β = 90 |
c = 153.535 | γ = 90 |
Symmetry | |
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Space Group | P 41 21 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 | ADSC QUANTUM 315 | Vertical focusing mirror; single crystal Si(311) bent monochromator (horizontal focusing) | 2007-02-02 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SSRL BEAMLINE BL9-1 | 0.979 | SSRL | BL9-1 |
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 | 3.37 | 27.16 | 99.7 | 0.068 | 8.1 | 4.5 | 16390 | 16341 | 108.222 |
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) | |||||||||||
3.37 | 3.55 | 100 | 0.463 | 1.8 | 4.8 | 2339 |
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-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB ENTRY 1XME | 3.37 | 26.96 | 16297 | 16329 | 823 | 99.84 | 0.2922 | 0.3355 | RANDOM | 85.48 |
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] | |
-0.04 | -0.04 | 0.07 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 36.125 |
r_dihedral_angle_3_deg | 19.271 |
r_dihedral_angle_4_deg | 18.676 |
r_dihedral_angle_1_deg | 5.323 |
r_angle_refined_deg | 1.304 |
r_nbtor_refined | 0.311 |
r_symmetry_vdw_refined | 0.277 |
r_metal_ion_refined | 0.211 |
r_nbd_refined | 0.207 |
r_xyhbond_nbd_refined | 0.127 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 5907 |
Nucleic Acid Atoms | |
Solvent Atoms | |
Heterogen Atoms | 118 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
Blu-Ice | data collection |
MOSFLM | data reduction |
SCALA | data scaling |
MOLREP | phasing |
REFMAC | phasing |
CNS | phasing |
Coot | model building |
CNS | refinement |