3LHY
Crystal structure of the mutant I199A of orotidine 5'-monophosphate decarboxylase from Methanobacterium thermoautotrophicum complexed with inhibitor BMP
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3G18 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 5.5 | 293 | 25% PEG 3350, 0,1M Bis-Tris, 0.2 M Ammonium sulfate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.15 | 42.77 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 59.758 | α = 90 |
b = 64.042 | β = 115.67 |
c = 61.917 | 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 | ADSC QUANTUM 4 | 2009-08-07 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | NSLS BEAMLINE X4A | 0.97915 | NSLS | X4A |
Data Collection
Overall | |||||||||||||||||||
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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 | 1.4 | 25 | 97.4 | 0.067 | 80756 | 80756 | 15.5 |
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 (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 3G18 | 1.4 | 22.77 | 80756 | 80756 | 4041 | 97.4 | 0.229 | 0.228 | 0.228 | 0.251 | RANDOM | 15.9 |
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] | |
-3.47 | -2.28 | 2.19 | 1.28 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
c_dihedral_angle_d | 21.8 |
c_scangle_it | 2.46 |
c_scbond_it | 1.76 |
c_mcangle_it | 1.41 |
c_angle_deg | 1.2 |
c_mcbond_it | 1.02 |
c_improper_angle_d | 0.93 |
c_bond_d | 0.005 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3293 |
Nucleic Acid Atoms | |
Solvent Atoms | 235 |
Heterogen Atoms | 44 |
Software
Software | |
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Software Name | Purpose |
ADSC | data collection |
BALBES | phasing |
CNS | refinement |
DENZO | data reduction |
SCALEPACK | data scaling |