3I8A
Staphylococcus aureus H30N, F98Y Dihydrofolate Reductase complexed with NADPH and 2,4-diamino-5-(3-(2,5-dimethoxyphenyl)prop-1-ynyl)-6-ethylpyrimidine (UCP120B)
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
---|---|---|---|
Type | Source | Accession Code | Details |
experimental model | PDB | 3FQO |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6.5 | 277 | 15% PEG 10,000, 150 mM sodium acetate, 100 mM MES pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
2.74 | 55.05 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 79.164 | α = 90 |
b = 79.164 | β = 90 |
c = 108.96 | γ = 120 |
Symmetry | |
---|---|
Space Group | P 61 2 2 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 77.2 | CCD | ADSC QUANTUM 315 | 2009-01-30 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | NSLS BEAMLINE X29A | 1.0809 | NSLS | X29A |
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 | 2.41 | 37.22 | 95.01 | 0.04 | 0.04 | 1.1 | 10.4 | 7504 | 7504 | 3 | 3 | 15.689 |
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 | 2.41 | 2.472 | 100 | 0.074 | 0.074 | 0.8 | 10.1 | 560 |
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 | Difference Fourier Methods | THROUGHOUT | 3FQO | 2.41 | 37.22 | 7504 | 7504 | 363 | 95.01 | 0.208 | 0.208 | 0.206 | 0.261 | RANDOM | 15.662 |
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] | |
-0.01 | -0.01 | -0.01 | 0.02 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 37.063 |
r_dihedral_angle_4_deg | 20.893 |
r_dihedral_angle_3_deg | 18.586 |
r_dihedral_angle_1_deg | 7.585 |
r_scangle_it | 2.709 |
r_scbond_it | 1.777 |
r_angle_refined_deg | 1.64 |
r_mcangle_it | 1.314 |
r_mcbond_it | 0.753 |
r_nbtor_refined | 0.308 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 1272 |
Nucleic Acid Atoms | |
Solvent Atoms | 43 |
Heterogen Atoms | 71 |
Software
Software | |
---|---|
Software Name | Purpose |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
CBASS | data collection |
HKL-2000 | data reduction |
SCALEPACK | data scaling |
Coot | model building |