1B5M
RAT OUTER MITOCHONDRIAL MEMBRANE CYTOCHROME B5
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3B5C | PDB ENTRY 3B5C |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | vapor diffusion with slow evaporation | 6.5 | CRYSTALS WERE OBTAINED BY VAPOR DIFFUSION TOGETHER WITH SLOW EVAPORATION USING 20% PEG 8000 IN 0.1M SODIUM CACODYLATE (PH = 6.5 WITH 0.2 M MAGNESIUM ACETATE., vapor diffusion with slow evaporation |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.56 | 52.02 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 30 | α = 90 |
b = 30 | β = 90 |
c = 219 | γ = 90 |
Symmetry | |
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Space Group | P 43 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 | 298 | AREA DETECTOR | SIEMENS | 1996-04-18 | M |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU |
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 | 2.7 | 20 | 96 | 0.049 | 1.5 | 2.5 | 3123 | 36 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
2.7 | 3.05 | 85 | 0.088 | 1 | 4 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Work (Depositor) | R-Free (Depositor) | Mean Isotropic B | ||||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | PDB ENTRY 3B5C | 2.7 | 20 | 3123 | 3123 | 3123 | 96 | 0.22 |
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] | |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
t_dihedral_angle_d | 20 |
t_it | 4.99 |
t_angle_deg | 2.9 |
t_nbd | 0.023 |
t_bond_d | 0.016 |
t_gen_planes | 0.012 |
t_trig_c_planes | 0.007 |
t_incorr_chiral_ct | |
t_pseud_angle |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 676 |
Nucleic Acid Atoms | |
Solvent Atoms | |
Heterogen Atoms | 43 |
Software
Software | |
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Software Name | Purpose |
MRCHK | model building |
TNT | refinement |
FRAMBO | data reduction |
SADIE | data reduction |
SAINT | data scaling |
MRCHK | phasing |