3CLZ
The set and ring associated (SRA) domain of UHRF1 bound to methylated DNA
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3BI7 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7 | 298 | 12 % PEG 1500, 0.1 M BIS-TRIS, 0.2 M NACL, 0.001 M TCEP, pH 7.00, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.25 | 61.84 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 76.198 | α = 90 |
b = 111.359 | β = 90.53 |
c = 97.403 | γ = 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 | 100 | CCD | MARMOSAIC 300 mm CCD | MIRRORS | 2008-02-15 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 23-ID-B | 0.96863 | APS | 23-ID-B |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 40 | 99.2 | 0.165 | 9.77 | 4.2 | 81560 | 81560 | -3 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
2.2 | 2.28 | 95 | 0.715 | 1.35 | 3.1 |
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 | MOLECULAR REPLACEMENT | THROUGHOUT | 3BI7 | 2.2 | 38.63 | 81444 | 77359 | 4085 | 99 | 0.19097 | 0.1888 | 0.23147 | RANDOM | 35.141 |
Temperature Factor Modeling | ||||||
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Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
0.14 | -0.01 | -0.14 | -0.01 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 36.062 |
r_dihedral_angle_3_deg | 16.226 |
r_dihedral_angle_4_deg | 14.234 |
r_dihedral_angle_1_deg | 5.963 |
r_scangle_it | 3.792 |
r_scbond_it | 2.798 |
r_mcangle_it | 2.271 |
r_angle_refined_deg | 1.665 |
r_mcbond_it | 1.457 |
r_nbtor_refined | 0.307 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 6490 |
Nucleic Acid Atoms | 1948 |
Solvent Atoms | 652 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
PHASER | phasing |
REFMAC | refinement |
HKL-2000 | data collection |
HKL-2000 | data reduction |
HKL-2000 | data scaling |