2YQH
Crystal structure of uridine-diphospho-N-acetylglucosamine pyrophosphorylase from Candida albicans, in the substrate-binding form
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2YQC | PDB ENTRY 2YQC |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 5.7 | 293 | 30% PEG 6000, 0.1M ammonium sulfate, 5% glycerol, 0.01M N-acetylglucosamine-1-phosphate, 0.1M citrate, pH 5.7, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.4 | 48.67 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 47.431 | ¦Á = 90.01 |
b = 61.804 | ¦Â = 97.72 |
c = 90.438 | ¦Ã = 92.88 |
Symmetry | |
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Space Group | P 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 | 95 | CCD | RIGAKU JUPITER 210 | 2004-12-06 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SPRING-8 BEAMLINE BL45XU | 1.0000 | SPring-8 | BL45XU |
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 | 2.3 | 50 | 93 | 0.07 | 11.2 | 2 | 43334 | 16.6 |
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) | |||||||||||
1 | 2.3 | 2.38 | 86.2 | 0.12 | 6.8 | 2 |
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 | MOLECULAR REPLACEMENT | THROUGHOUT | PDB ENTRY 2YQC | 2.3 | 38.31 | 44027 | 2188 | 97.7 | 0.193 | 0.193 | 0.238 | RANDOM | 22.9 |
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] | |
2.13 | 1.29 | 1.24 | 0.63 | -0.63 | -2.76 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
c_dihedral_angle_d | 894.2 |
c_scangle_it | 3.1 |
c_scbond_it | 2.15 |
c_mcangle_it | 2.1 |
c_angle_deg | 1.4 |
c_mcbond_it | 1.35 |
c_bond_d | 0.009 |
c_bond_d_na | |
c_bond_d_prot | |
c_angle_d |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 7259 |
Nucleic Acid Atoms | |
Solvent Atoms | 257 |
Heterogen Atoms | 55 |
Software
Software | |
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Software Name | Purpose |
CNS | refinement |
HKL-2000 | data collection |
HKL-2000 | data reduction |
SCALEPACK | data scaling |
AMoRE | phasing |