2FHK
Crystal structure of formylmethanofuran: tetrahydromethanopterin formyltransferase in complex with its coenzymes
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1FTR | PDB ID 1FTR |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7 | 298 | 12-18 % PEG 8000, 20 % glycerol, 0.5 M KCl, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.39 | 48.51 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 86 | ¦Á = 90 |
b = 74.2 | ¦Â = 113.6 |
c = 103.6 | ¦Ã = 90 |
Symmetry | |
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Space Group | P 1 21 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 | 281 | CCD | ADSC QUANTUM 4 | 2004-04-14 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID14-4 | 0.91 | ESRF | ID14-4 |
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 | 104 | 98.1 | 0.156 | 7.64 | 80885 |
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) | |||||||||||
2 | 2.1 | 96.6 | 0.443 | 3.91 | 10589 |
Refinement
Statistics | |||||||||||||||||||
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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-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB ID 1FTR | 2 | 20 | 80587 | 80587 | 4030 | 99.75 | 0.219 | 0.219 | 0.218 | 0.245 | RANDOM | 19.398 |
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] | |
2.64 | 1.07 | -0.8 | -0.98 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.6 |
r_dihedral_angle_3_deg | 13.171 |
r_dihedral_angle_4_deg | 11.879 |
r_scangle_it | 6.502 |
r_dihedral_angle_1_deg | 5.347 |
r_scbond_it | 4.016 |
r_mcangle_it | 2.175 |
r_angle_refined_deg | 1.152 |
r_mcbond_it | 1.087 |
r_nbtor_refined | 0.301 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 8897 |
Nucleic Acid Atoms | |
Solvent Atoms | 474 |
Heterogen Atoms | 113 |
Software
Software | |
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Software Name | Purpose |
DENZO | data reduction |
XSCALE | data scaling |
EPMR | phasing |
REFMAC | refinement |