2HF9
Crystal structure of HypB from Methanocaldococcus jannaschii in the triphosphate form
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2HF8 | PDB entry: 2Hf8 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION | 293 | 150 mM maleic acid disodium salt, 42.5 mM HCl, 20% PEG3350, VAPOR DIFFUSION, temperature 293K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.33 | 47.19 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 43.463 | ¦Á = 90 |
b = 68.107 | ¦Â = 90 |
c = 155.84 | ¦Ã = 90 |
Symmetry | |
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Space Group | P 21 21 21 |
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 | 2005-02-08 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID14-1 | 0.9758 | ESRF | ID14-1 |
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 | 2.1 | 20 | 98.6 | 0.048 | 20.54 | 6.5 | 51141 | 51141 | 3 | 24.484 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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) | |||||||||||
2.1 | 2.2 | 93.1 | 0.084 | 9.3 | 6.4 | 6342 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB entry: 2Hf8 | 1.9 | 19.96 | 37222 | 37222 | 3723 | 100 | 0.22 | 0.217 | 0.241 | RANDOM | 16.316 |
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] | |
0.8 | -0.28 | -0.53 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 33.368 |
r_dihedral_angle_4_deg | 17.76 |
r_dihedral_angle_3_deg | 13.069 |
r_dihedral_angle_1_deg | 5.269 |
r_scangle_it | 1.732 |
r_angle_refined_deg | 1.104 |
r_scbond_it | 1.032 |
r_mcangle_it | 0.733 |
r_mcbond_it | 0.439 |
r_nbtor_refined | 0.293 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3246 |
Nucleic Acid Atoms | |
Solvent Atoms | 174 |
Heterogen Atoms | 68 |
Software
Software | |
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Software Name | Purpose |
XSCALE | data scaling |
SOLVE | phasing |
RESOLVE | phasing |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
XDS | data reduction |