1BU5
X-RAY CRYSTAL STRUCTURE OF THE DESULFOVIBRIO VULGARIS (HILDENBOROUGH) APOFLAVODOXIN-RIBOFLAVIN COMPLEX
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 7 | CRYSTALS WERE GROWN USING THE HANGING DROP METHOD OF VAPOUR DIFFUSION FROM TRIALS WITH AMMONIUM SULPHATE IN THE CONCENTRATION RANGE 60-80% SATURATION IN 50MM SODIUM PHOSPHATE BUFFER PH 8.0 CONTAINING 1MM EDTA WITH A PROTEIN CONCENTRATION OF 10-15MG/ML. CRYSTALS APPEAR OVER 1-3 DAYS., pH 7.0 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.75 | 55 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 94.38 | α = 90 |
b = 62.31 | β = 127.26 |
c = 77.42 | γ = 90 |
Symmetry | |
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Space Group | C 1 2 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 | 295 | IMAGE PLATE | MARRESEARCH | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SRS BEAMLINE PX9.5 | SRS | PX9.5 |
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 | 1.83 | 20 | 79.9 | 0.042 | 15.3 | 1.5 | 26539 | -3 | 23 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 1.83 | 1.86 | 83.2 | 0.23 | 2.5 | 1.5 |
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 | WILD TYPE FLAVODOXIN COORDINATES NOT DEPOSITED [M.A.WALSH PH.D THESIS NATIONAL UNIVERSITY OF IRELAND (1994)] BUT ESSENTIALLY IDENTICAL TO PDB ENTRY 2FX2 | 1.83 | 10 | 26539 | 2037 | 81 | 0.169 | 0.167 | 0.202 | RANDOM | 27.1 |
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] | |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
p_transverse_tor | 25.46 |
p_staggered_tor | 20.18 |
p_scangle_it | 10.3 |
p_scbond_it | 6.8 |
p_mcangle_it | 4.4 |
p_mcbond_it | 3.18 |
p_planar_tor | 2.3 |
p_multtor_nbd | 0.25 |
p_singtor_nbd | 0.23 |
p_chiral_restr | 0.17 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2208 |
Nucleic Acid Atoms | |
Solvent Atoms | 197 |
Heterogen Atoms | 64 |
Software
Software | |
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Software Name | Purpose |
AMoRE | phasing |
CCP4 | refinement |
DENZO | data reduction |
SCALEPACK | data scaling |