4QPP
The Crystal Structure of Human HMT1 hnRNP methyltransferase-like protein 6 in complex with compound DS-421 (2-{4-[3-CHLORO-2-(2-METHOXYPHENYL)-1H-INDOL-5-YL]PIPERIDIN-1-YL}-N-METHYLETHANAMINE
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 4HC4 | pdb entry 4HC4 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 4.6 | 291 | 2.0 M NaForm, 0.1 M NaoAc, pH 4.6, vapor diffusion hanging drop, temperature 291K, VAPOR DIFFUSION, HANGING DROP |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.35 | 47.67 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 133.884 | α = 90 |
b = 133.884 | β = 90 |
c = 133.419 | γ = 90 |
Symmetry | |
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Space Group | P 42 2 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 | ADSC QUANTUM 315r | 2014-03-20 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 19-ID | 0.97856 | APS | 19-ID |
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 | 2.52 | 50 | 100 | 0.133 | 6.1 | 8.1 | 336892 | 41807 | 33.3 |
Highest Resolution Shell | |||||||||||||||||||
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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 | 2.52 | 2.56 | 100 | 0.904 | 8.2 | 2051 |
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 | MOLECULAR REPLACEMENT | THROUGHOUT | pdb entry 4HC4 | 2.52 | 50 | 41519 | 830 | 99.87 | 0.1915 | 0.1907 | 0.2345 | RANDOM | 37.597 |
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] | |
-0.25 | -0.25 | 0.49 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 34.876 |
r_dihedral_angle_4_deg | 14.805 |
r_dihedral_angle_3_deg | 13.154 |
r_dihedral_angle_1_deg | 5.28 |
r_mcangle_it | 2.248 |
r_mcbond_it | 1.295 |
r_mcbond_other | 1.294 |
r_angle_refined_deg | 1.117 |
r_angle_other_deg | 0.893 |
r_chiral_restr | 0.061 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 7685 |
Nucleic Acid Atoms | |
Solvent Atoms | 282 |
Heterogen Atoms | 155 |
Software
Software | |
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Software Name | Purpose |
SCALEPACK | data scaling |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
SBC-Collect | data collection |
HKL-3000 | data reduction |
HKL-3000 | data scaling |
PHASER | phasing |
Coot | model building |