7MX6
Leishmania major dihydroorotate dehydrogenase in complex with [4-(1H-pyrrol-1-yl)phenyl]methanol
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3GYE | PDB entry 3GYE |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 295 | 100 mM sodium citrate tribasic dihydrate, pH 5.6, 1.3 M lithium sulfate, 0.30 M ammonium sulfate |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.88 | 57.35 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 142.195 | ¦Á = 90 |
b = 142.195 | ¦Â = 90 |
c = 68.735 | ¦Ã = 120 |
Symmetry | |
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Space Group | P 61 |
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 | MAR CCD 165 mm | 2011-02-28 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | LNLS BEAMLINE D03B-MX1 | 1.437 | LNLS | D03B-MX1 |
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 | 1.8 | 35.24 | 100 | 0.085 | 0.085 | 14.8 | 6.4 | 73441 |
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 | 1.8 | 1.9 | 98.8 | 0.704 | 0.704 | 2.5 | 6 |
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 (All) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | PDB entry 3GYE | 1.8 | 35.24 | 73409 | 3702 | 99.969 | 0.164 | 0.1627 | 0.1844 | 5.04 | 20.497 |
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] | |
-0.02 | -0.01 | -0.02 | 0.065 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 38.914 |
r_dihedral_angle_4_deg | 14.539 |
r_dihedral_angle_3_deg | 12.002 |
r_dihedral_angle_1_deg | 7.061 |
r_lrange_it | 3.939 |
r_lrange_other | 3.88 |
r_scangle_it | 2.465 |
r_scangle_other | 2.465 |
r_mcangle_other | 1.684 |
r_mcangle_it | 1.683 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4626 |
Nucleic Acid Atoms | |
Solvent Atoms | 382 |
Heterogen Atoms | 128 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
MOSFLM | data reduction |
SCALA | data scaling |
MOLREP | phasing |