2BB6
Structure of Cobalamin-complexed Bovine Transcobalamin in Monoclinic Crystal Form
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 8.5 | 293 | 28% PEG 8000, 0.2M magnesium acetate, 20% 2-methyl-2,4-pentadiol, 0.1M TRIS, VAPOR DIFFUSION, HANGING DROP, temperature 293K, pH 8.50 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.56 | 51.95 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 95.826 | α = 90 |
b = 100.664 | β = 97.16 |
c = 99.143 | γ = 90 |
Symmetry | |
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Space Group | P 1 21 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 | MARRESEARCH | 2002-12-13 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ELETTRA BEAMLINE 5.2R | ELETTRA | 5.2R |
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 | 2 | 18 | 96.8 | 0.097 | 0.097 | 12 | 3.5 | 121830 | 25.8 |
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 | 2 | 2.07 | 93.3 | 0.522 | 0.522 | 2.2 | 3.2 |
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-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | UNREFINED PARTIAL MODEL FROM PHASING WITH SHARP V2.0 USING SINGLE-WAVELENGTH ANOMALOUS DISPERSION DATA | 2 | 18 | 116949 | 116949 | 4895 | 96.8 | 0.243 | 0.241 | 0.28 | RANDOM | 32.24 |
Temperature Factor Modeling | ||||||
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Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
0.79 | 0.27 | -1.06 | 0.33 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 39.024 |
r_dihedral_angle_4_deg | 23.697 |
r_dihedral_angle_3_deg | 20.727 |
r_dihedral_angle_1_deg | 6.996 |
r_scangle_it | 3.192 |
r_scbond_it | 1.953 |
r_mcangle_it | 1.489 |
r_angle_refined_deg | 1.355 |
r_mcbond_it | 0.789 |
r_nbtor_refined | 0.299 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 13016 |
Nucleic Acid Atoms | |
Solvent Atoms | 764 |
Heterogen Atoms | 368 |
Software
Software | |
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Software Name | Purpose |
DENZO | data reduction |
SCALEPACK | data scaling |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
AMoRE | phasing |