5PIV
PanDDA analysis group deposition -- Crystal Structure of JMJD2D after initial refinement with no ligand modelled (structure 44)
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7 | 298 | 28% PEG3350 -- 0.1M HEPES pH 7.0 -- 0.25M ammonium sulfate |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.26 | 45.63 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 71.225 | α = 90 |
b = 71.225 | β = 90 |
c = 150.015 | γ = 90 |
Symmetry | |
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Space Group | P 43 21 2 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | PIXEL | DECTRIS PILATUS 6M | 2012-12-15 | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I03 | 0.97630 | Diamond | I03 |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | 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 | 1.43 | 29.32 | 99.8 | 0.065 | 0.068 | 0.019 | 1 | 24.9 | 12.8 | 72137 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||
1 | 1.43 | 1.46 | 96.1 | 0.81 | 0.853 | 0.265 | 0.834 | 10.1 | 3651 |
Refinement
Statistics | |||||||||||||||||||
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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 | FOURIER SYNTHESIS | THROUGHOUT | 4D6R | 1.43 | 29.32 | 68503 | 3536 | 99.75 | 0.1576 | 0.1563 | 0.1821 | RANDOM | 18.126 |
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] | |
0.25 | 0.25 | -0.49 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 36.405 |
r_dihedral_angle_4_deg | 18.498 |
r_dihedral_angle_3_deg | 12.1 |
r_dihedral_angle_1_deg | 6.819 |
r_mcangle_it | 2.953 |
r_angle_refined_deg | 2.334 |
r_mcbond_it | 2 |
r_mcbond_other | 1.995 |
r_angle_other_deg | 1.202 |
r_chiral_restr | 0.151 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2664 |
Nucleic Acid Atoms | |
Solvent Atoms | 442 |
Heterogen Atoms | 60 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
Aimless | data scaling |
PDB_EXTRACT | data extraction |
XDS | data reduction |
REFMAC | phasing |