2V3N
Crystallographic analysis of upper axial ligand substitutions in cobalamin bound to transcobalamin
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | 8.5 | PROTEIN AT 0.5 MM IN 1 M NACL, 0.1 M TRIS, PH 7.5 CRYSTALLIZED FROM 28% PEG 8000, 0.2 M MAGNESIUM ACETATE, 0.1 M TRIS PH 8.5, 20% 2-METHYL-2, 4-PENTADIOL, 15 MM KCN |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
4.1 | 69.9 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 100.83 | α = 90 |
b = 100.83 | β = 90 |
c = 130.215 | γ = 120 |
Symmetry | |
---|---|
Space Group | P 31 2 1 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | CCD | MARRESEARCH | 2007-04-04 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ELETTRA BEAMLINE 5.2R | ELETTRA | 5.2R |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 2.7 | 20.7 | 99.3 | 0.12 | 9.7 | 3.1 | 21370 |
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 | 2.7 | 2.85 | 99.9 | 0.75 | 1.7 | 3.1 |
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 2BBC | 2.73 | 20.7 | 20574 | 857 | 99.3 | 0.213 | 0.211 | 0.251 | RANDOM | 43.4 |
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] | |
0.433 | 0.216 | 0.433 | -0.649 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 37.867 |
r_dihedral_angle_4_deg | 20.715 |
r_dihedral_angle_3_deg | 17.011 |
r_dihedral_angle_1_deg | 5.771 |
r_scangle_it | 2.275 |
r_scbond_it | 1.319 |
r_angle_refined_deg | 1.308 |
r_mcangle_it | 1.181 |
r_mcbond_it | 0.661 |
r_nbtor_refined | 0.305 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 3178 |
Nucleic Acid Atoms | |
Solvent Atoms | 174 |
Heterogen Atoms | 96 |
Software
Software | |
---|---|
Software Name | Purpose |
REFMAC | refinement |
MOSFLM | data reduction |
SCALA | data scaling |
REFMAC | phasing |