1XRH
Crystal Structure of Ureidoglycolate Dehydrogenase from Escherichia Coli
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1RFM | Density modified experimental electron density map based on Se sites. Se sites were obtained from poor phases from a weak MR solution using a model derived from pdb entry 1RFM. |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 5.6 | 291 | 15% PEG 4000, 0.1M Sodium Citrate pH 5.6, 0.06M Amonium Acetate, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.38 | 47.9 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 104.715 | α = 90 |
b = 129.916 | β = 95.77 |
c = 106.468 | 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 | Diamond monochromator and downstream mirror | 2003-10-31 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 31-ID | 0.9800 | APS | 31-ID |
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 | 2.25 | 19.86 | 80.5 | 0.078 | 6.5 | 1.2 | 213051 | 213051 | 25.6 |
Highest Resolution Shell | |||||||||||||||||||
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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) | |||||||||||
2.25 | 2.33 | 72 | 0.284 | 19123 |
Refinement
Statistics | |||||||||||||||||||
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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 | SAD | THROUGHOUT | Density modified experimental electron density map based on Se sites. Se sites were obtained from poor phases from a weak MR solution using a model derived from pdb entry 1RFM. | 2.25 | 19.86 | 200433 | 9082 | 75.6 | 0.1921 | 0.192 | 0.25 | RANDOM | 38.6 |
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] | |
-0.44 | 1.74 | 3.28 | -2.85 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
c_dihedral_angle_d | 23.9 |
c_scangle_it | 3.87 |
c_scbond_it | 3.09 |
c_mcangle_it | 2.22 |
c_angle_deg | 1.8 |
c_mcbond_it | 1.44 |
c_improper_angle_d | 1.22 |
c_bond_d | 0.018 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 20836 |
Nucleic Acid Atoms | |
Solvent Atoms | 644 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
DENZO | data reduction |
SCALEPACK | data scaling |
MOLREP | phasing |
BEAST | model building |
SHARP | phasing |
RESOLVE | model building |
CNS | refinement |
BEAST | phasing |
RESOLVE | phasing |