4RB2
Crystal structure of Magnetospirillum gryphiswaldense MSR-1 SeMet-Fur-Mn2+-feoAB1 operator
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 4RAY | PDB entry 4RAY |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6 | 277 | pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.58 | 52.32 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 94.301 | α = 90 |
b = 68.669 | β = 109.25 |
c = 82.646 | 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 | 130 | CCD | ADSC QUANTUM 210 | 2012-06-11 | M | MAD |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | BSRF BEAMLINE 1W2B | 0.9793, 0.9795, 1.000 | BSRF | 1W2B |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 2.82 | 50 | 91.4 | 12295 | 11230 | 3 | 3 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||||
1 | 2.82 | 2.87 | 92.4 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | Number Reflections (All) | 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 | MAD | THROUGHOUT | PDB entry 4RAY | 2.82 | 45.73 | 3 | 11230 | 10544 | 580 | 91.36 | 0.24013 | 0.23811 | 0.27541 | RANDOM | 85.68 |
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] | |
-6.48 | 5.08 | -1.46 | 4.96 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 33.754 |
r_dihedral_angle_3_deg | 17.882 |
r_dihedral_angle_4_deg | 16.016 |
r_dihedral_angle_1_deg | 4.688 |
r_angle_refined_deg | 0.866 |
r_chiral_restr | 0.058 |
r_bond_refined_d | 0.004 |
r_gen_planes_refined | 0.004 |
r_bond_other_d | |
r_angle_other_deg |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2033 |
Nucleic Acid Atoms | 1019 |
Solvent Atoms | 14 |
Heterogen Atoms | 4 |
Software
Software | |
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Software Name | Purpose |
ADSC | data collection |
SHARP | phasing |
REFMAC | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |