3DAF
The crystal structure of [Fe]-hydrogenase holoenzyme (HMD) from METHANOCALDOCOCCUS JANNASCHII cocrystallized with cyanide
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2BOJ | PDB ENTRY 2BOJ |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 8.5 | 283 | 50% MPD, 0.1M TRIS/HCL, 20mM NH4H2PO4, cyanide, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 283K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.64 | 53.42 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 97.14 | α = 90 |
b = 97.14 | β = 90 |
c = 166.03 | γ = 90 |
Symmetry | |
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Space Group | I 41 2 2 |
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 | MARMOSAIC 225 mm CCD | mirrors | 2007-02-01 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SLS BEAMLINE X10SA | 0.99198 | SLS | X10SA |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (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 | 1.75 | 30 | 0.901 | 0.065 | 0.065 | 18.3 | 6.1 | 36729 | 36729 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 1.75 | 1.8 | 73.1 | 0.49 | 0.51 | 4 | 5.2 | 2389 |
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 ENTRY 2BOJ | 1.75 | 10 | 36673 | 36673 | 1944 | 96.31 | 0.1883 | 0.1883 | 0.18653 | 0.22154 | RANDOM | 34.124 |
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] | |
0.2 | 0.2 | -0.4 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 39.785 |
r_dihedral_angle_4_deg | 19.369 |
r_dihedral_angle_3_deg | 14.394 |
r_dihedral_angle_1_deg | 5.372 |
r_scangle_it | 4.057 |
r_scbond_it | 2.613 |
r_angle_refined_deg | 1.722 |
r_mcangle_it | 1.541 |
r_mcbond_it | 1.064 |
r_nbtor_refined | 0.3 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2591 |
Nucleic Acid Atoms | |
Solvent Atoms | 214 |
Heterogen Atoms | 49 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
MAR345dtb | data collection |
XDS | data reduction |
XDS | data scaling |
EPMR | phasing |