1DWK
STRUCTURE OF CYANASE WITH THE DI-ANION OXALATE BOUND AT THE ENZYME ACTIVE SITE
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7.3 | SELENOMETHIONINE LABELLED CRYSTALS WERE GROWN BY THE SITTING DROP METHOD OF VAPOUR DIFFUSION FROM 50% AMMONIUM SULPHATE SOLUTIONS BUFFERED WITH 50MM NAKPO4, PH = 7.3, AND IN THE PRESENCE OF 50 MM TRIC/HCL, PH =7.3. MICROSEEDING WITH WILD-TYPE CRYSTALS PRODUCED CRYSTALS THAT GREW TO 0.1 X 0.2 X 0.7 MM**3 OVER 5-7 DAYS. CRYSTALS WERE THEN SOAKED FOR 4 HOURS IN 5 MM SODIUM OXALATE BEFORE BEING FLASH FROZEN. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.53 | 51 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 76.33 | α = 70.1 |
b = 80.93 | β = 71.95 |
c = 82.13 | γ = 66.42 |
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 | 100 | CCD | ARGONNE APS-1 | MIRROR | 1998-11-15 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 19-ID | APS | 19-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 | 1.65 | 20 | 95.4 | 0.047 | 26.4 | 2.3 | 190231 | 13.4 |
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 | 1.65 | 1.68 | 79.4 | 0.171 | 3.9 | 1.9 |
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 1DW9 | 1.65 | 20 | 190161 | 9561 | 95.4 | 0.138 | 0.146 | 0.181 | RANDOM | 15.8 |
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] | |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
p_transverse_tor | 20.2 |
p_staggered_tor | 12.7 |
p_planar_tor | 6.6 |
p_scangle_it | 3.22 |
p_scbond_it | 2.41 |
p_mcangle_it | 1.79 |
p_mcbond_it | 1.38 |
p_multtor_nbd | 0.258 |
p_singtor_nbd | 0.186 |
p_chiral_restr | 0.155 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 11970 |
Nucleic Acid Atoms | |
Solvent Atoms | 2464 |
Heterogen Atoms | 145 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
CCP4 | phasing |