3V1Z
Crystal structure of Type IIF restriction endonuclease Bse634I with cognate DNA
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1KNV | PDB ENTRY 1KNV |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 5.5 | 293 | 100mM Na-acetate pH 4.25-5.5, 10mM CaCl2 or CaAc2, 4-8% (w/v) of PEG8000, temperature 293K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.4 | 49.2 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 72.008 | α = 90 |
b = 83.632 | β = 90 |
c = 123.336 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 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 | 2005-11-07 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | EMBL/DESY, HAMBURG BEAMLINE X12 | EMBL/DESY, HAMBURG | X12 |
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 | 2.2 | 69.14 | 99.1 | 0.067 | 0.067 | 16.7 | 3.8 | 33372 | 39.35 |
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 | 2.3 | 2.42 | 95.2 | 0.307 | 0.307 | 2.5 | 3.3 |
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 (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||
X-RAY DIFFRACTION | THROUGHOUT | PDB ENTRY 1KNV | 2.2 | 62.14 | 38563 | 33238 | 3719 | 95.9 | 0.232 | 0.226 | 0.283 | RANDOM | 42.3 |
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] | |
-1.34 | 3.75 | -2.41 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 33.749 |
r_dihedral_angle_4_deg | 16.181 |
r_dihedral_angle_3_deg | 14.788 |
r_dihedral_angle_1_deg | 5.267 |
r_scangle_it | 1.156 |
r_angle_refined_deg | 1.009 |
r_scbond_it | 0.721 |
r_mcangle_it | 0.604 |
r_mcbond_it | 0.329 |
r_chiral_restr | 0.065 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4695 |
Nucleic Acid Atoms | 526 |
Solvent Atoms | 218 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
MOSFLM | data reduction |
SCALA | data scaling |
PDB_EXTRACT | data extraction |
MOLREP | phasing |