4Z0R
Crystal Structure of the CW domain of ZCWPW2 mutant F78R in complex with histone H3 peptide
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 4O62 | PDB entry 4O62 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7.5 | 293 | 2 M ammonium sulfate, 2% PEG400, 0.1 M HEPES sodium |
Crystal Properties | |
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Matthews coefficient | Solvent content |
4.5 | 72.3 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 126.659 | α = 90 |
b = 126.659 | β = 90 |
c = 63.271 | γ = 120 |
Symmetry | |
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Space Group | H 3 |
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 | ADSC QUANTUM 315r | 2014-06-13 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 19-ID | 0.9786 | APS | 19-ID |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rpim I (All) | CC (Half) | 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 | 41.442 | 99.4 | 0.073 | 0.035 | 0.998 | 14.3 | 5.5 | 37974 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||
1 | 1.75 | 1.78 | 100 | 1.039 | 0.481 | 0.665 | 1.5 | 5.7 | 2114 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | 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 4O62 | 1.75 | 41.442 | 1580 | 99.38 | 0.1777 | 0.1771 | 0.1922 | THIN SHELLS (SFTOOLS) | 33.923 |
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] | |
-0.56 | -0.28 | -0.56 | 1.8 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 28.305 |
r_dihedral_angle_4_deg | 19.641 |
r_dihedral_angle_3_deg | 10.59 |
r_dihedral_angle_1_deg | 6.231 |
r_mcangle_it | 2.568 |
r_mcbond_it | 1.793 |
r_mcbond_other | 1.789 |
r_angle_refined_deg | 1.606 |
r_angle_other_deg | 0.982 |
r_chiral_restr | 0.108 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1483 |
Nucleic Acid Atoms | |
Solvent Atoms | 130 |
Heterogen Atoms | 36 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
Aimless | data scaling |
PDB_EXTRACT | data extraction |
XDS | data scaling |
Coot | model building |
PHASER | phasing |