1XDJ
Crystal Structure of T. maritima Cobalamin-Independent Methionine Synthase complexed with Zn2+ and Homocysteine
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR BATCH, UNDER OIL | 5.2 | 295 | PEG 4000, SODIUM ACETATE, AMMONIUM SULFATE, pH 5.2, VAPOR BATCH, UNDER OIL, temperature 295K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.33 | 49.24 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 167.053 | α = 90 |
b = 159.366 | β = 90 |
c = 65.639 | γ = 90 |
Symmetry | |
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Space Group | P 21 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 | MARMOSAIC 225 mm CCD | 2003-12-05 | M | MAD | ||||||
2 | 1 | 100 | CCD | MAR CCD 165 mm | 2003-11-16 |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 5ID-B | 0.9797 | APS | 5ID-B |
2 | SYNCHROTRON | APS BEAMLINE 32-ID | 0.9800 | APS | 32-ID |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 2.2 | 19.9 | 92.9 | 89637 | 83276 | 21 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||||
2.2 | 2.34 | 87.7 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Number Reflections (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 2.2 | 19.9 | 89637 | 83276 | 1666 | 92.9 | 0.247 | 0.227 | 0.227 | 0.268 | RANDOM | 25.6 |
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] | |
-1.25 | -0.56 | 1.81 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
c_dihedral_angle_d | 22.5 |
c_scangle_it | 3 |
c_scbond_it | 2.17 |
c_mcangle_it | 2.04 |
c_angle_deg | 1.3 |
c_mcbond_it | 1.29 |
c_improper_angle_d | 0.82 |
c_bond_d | 0.007 |
c_bond_d_na | |
c_bond_d_prot |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 11203 |
Nucleic Acid Atoms | |
Solvent Atoms | 298 |
Heterogen Atoms | 44 |
Software
Software | |
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Software Name | Purpose |
CNS | refinement |
MAR345 | data collection |
SCALEPACK | data scaling |
EPMR | phasing |