3CKK
Crystal structure of human methyltransferase-like protein 1
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7.5 | 297 | 2.0 M Ammonium sulfate, 2% PEG 400, 0.1 M Na HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 297K |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
2.39 | 48.59 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 90.316 | α = 90 |
b = 90.316 | β = 90 |
c = 54.94 | γ = 120 |
Symmetry | |
---|---|
Space Group | P 65 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | Si(111) | 2008-03-05 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 23-ID-B | 1.03310 | APS | 23-ID-B |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 1.55 | 100 | 99.1 | 0.068 | 0.068 | 13.2 | 11.2 | 36869 | 36869 | 23.1 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 1.55 | 1.61 | 91.3 | 0.596 | 0.596 | 1.78 | 4.5 | 3389 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB entry 2VDU | 1.55 | 50 | 36089 | 36089 | 750 | 99.04 | 0.19962 | 0.19962 | 0.19922 | 0.21835 | RANDOM | 24.817 |
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] | |
-0.03 | -0.02 | -0.03 | 0.05 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 28.964 |
r_dihedral_angle_4_deg | 15.429 |
r_dihedral_angle_3_deg | 12.368 |
r_dihedral_angle_1_deg | 5.067 |
r_scangle_it | 2.708 |
r_scbond_it | 1.944 |
r_mcangle_it | 1.4 |
r_angle_refined_deg | 1.276 |
r_mcbond_it | 0.798 |
r_nbtor_refined | 0.309 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 1533 |
Nucleic Acid Atoms | |
Solvent Atoms | 235 |
Heterogen Atoms | 33 |
Software
Software | |
---|---|
Software Name | Purpose |
REFMAC | refinement |
Blu-Ice | data collection |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
PHASER | phasing |
ARP/wARP | model building |
Coot | model building |