3FD2
Crystal structure of mMsoI/DNA complex with calcium
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1M5X |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 7.3 | 291 | 22% PEG 400, 100 mM Tris pH 7.3, 10 mM calcium chloride, 20 mM sodium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
1.93 | 36.4 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 41.932 | α = 107.21 |
b = 41.933 | β = 95.43 |
c = 70.96 | γ = 109.44 |
Symmetry | |
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Space Group | P 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 | IMAGE PLATE | RIGAKU RAXIS IV | 2008-03-25 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | OTHER |
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 | 2.69 | 50 | 97 | 0.052 | 21 | 3.9 | 11073 |
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) | |||||||||||
1 | 2.69 | 2.8 | 95.8 | 0.258 | 4.51 | 3.9 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 1M5X | 2.69 | 50 | 10862 | 546 | 96.6 | 0.215 | 0.211 | 0.281 | RANDOM | 59.2 |
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] | |
2.72 | 4.6 | -6.76 | 1.75 | -3.57 | 0.12 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 34.787 |
r_dihedral_angle_1_deg | 5.122 |
r_angle_refined_deg | 1.11 |
r_nbtor_refined | 0.304 |
r_nbd_refined | 0.198 |
r_xyhbond_nbd_refined | 0.142 |
r_chiral_restr | 0.064 |
r_bond_refined_d | 0.008 |
r_gen_planes_refined | 0.003 |
r_bond_other_d |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2720 |
Nucleic Acid Atoms | 978 |
Solvent Atoms | 35 |
Heterogen Atoms | 2 |
Software
Software | |
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Software Name | Purpose |
HKL-2000 | data collection |
PHASES | phasing |
REFMAC | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |