1W7O
cytochrome c3 from Desulfomicrobium baculatus
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2CY3 | PDB ENTRY 2CY3 |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | 8 | 25% PEG 6K, 0.1 M TRIS-HCL, PH 7.5-8.0 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.66 | 53.3 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 43 | α = 90 |
b = 43 | β = 90 |
c = 64.7 | γ = 120 |
Symmetry | |
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Space Group | P 31 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 277 | IMAGE PLATE | MARRESEARCH | 1992-10-15 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SRS BEAMLINE PX9.5 | SRS | PX9.5 |
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 | 1.81 | 21.5 | 94.4 | 0.08 | 9.1 | 1.9 | 11633 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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) | |||||||||||
1 | 1.81 | 1.9 | 80 | 0.183 | 3 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 2CY3 | 1.81 | 20.41 | 10752 | 876 | 94.7 | 0.178 | 0.176 | 0.199 | RANDOM | 24.73 |
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 | -0.01 | -0.02 | 0.03 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_1_deg | 6.33 |
r_scangle_it | 4.218 |
r_scbond_it | 2.789 |
r_mcangle_it | 2.267 |
r_angle_refined_deg | 1.948 |
r_mcbond_it | 1.353 |
r_angle_other_deg | 1.069 |
r_nbd_refined | 0.398 |
r_symmetry_vdw_other | 0.377 |
r_nbd_other | 0.251 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 878 |
Nucleic Acid Atoms | |
Solvent Atoms | 72 |
Heterogen Atoms | 172 |
Software
Software | |
---|---|
Software Name | Purpose |
REFMAC | refinement |
DENZO | data reduction |
SCALEPACK | data scaling |
AMoRE | phasing |