2D4L
Crystal structure of truncated in C-terminal M-PMV dUTPase
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
---|---|---|---|
Type | Source | Accession Code | Details |
experimental model | PDB | 2AKV |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 8.5 | 293 | PEG 8000, AMMONIUM CHLORIDE, TRIS, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
2.14 | 42.54 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 61.163 | α = 90 |
b = 61.163 | β = 90 |
c = 64.167 | γ = 120 |
Symmetry | |
---|---|
Space Group | P 63 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | IMAGE PLATE | MARRESEARCH | 2005-01-19 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | EMBL/DESY, HAMBURG BEAMLINE BW7B | 0.843 | EMBL/DESY, HAMBURG | BW7B |
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 | 1.7 | 53 | 98.34 | 0.037 | 0.031 | 21.15 | 3.08 | 14813 | 14813 | -3 | 33.811 |
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 | 1.7 | 1.8 | 98 | 0.533 | 0.44 | 3.33 | 3.09 | 2308 |
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 | THROUGHOUT | 2AKV | 1.7 | 20 | 14013 | 14013 | 800 | 98.34 | 0.1632 | 0.1632 | 0.1623 | 0.17888 | RANDOM | 31.803 |
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] | |
1.22 | 0.61 | 1.22 | -1.83 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 41.506 |
r_scangle_it | 15.06 |
r_dihedral_angle_3_deg | 13.575 |
r_scbond_it | 12.776 |
r_dihedral_angle_1_deg | 12.202 |
r_dihedral_angle_4_deg | 9.046 |
r_mcangle_it | 5.274 |
r_mcbond_it | 2.338 |
r_angle_refined_deg | 1.948 |
r_nbtor_refined | 0.32 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 828 |
Nucleic Acid Atoms | |
Solvent Atoms | 124 |
Heterogen Atoms |
Software
Software | |
---|---|
Software Name | Purpose |
REFMAC | refinement |
MAR345 | data collection |
XDS | data scaling |