3PMF
Crystal structure of Staphylococcal nuclease variant Delta+PHS V23A at cryogenic temperature
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
---|---|---|---|
Type | Source | Accession Code | Details |
experimental model | PDB | 3BDC | 3BDC with all H2Os, Ca2+ and THP removed and the following truncations: H8A, T13A, V23A, Q30A, K64A, T82A, Y113A, V114A, Y115A; all b-factors were reset to 20A2. |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7 | 277 | 22% MPD, 25 mM Potassium Phosphate, Calcium Chloride, pdTp, pH 7.0, vapor diffusion, hanging drop, temperature 277K |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
2.2 | 44.04 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 31.09 | α = 90 |
b = 60.186 | β = 94.69 |
c = 37.987 | γ = 90 |
Symmetry | |
---|---|
Space Group | P 1 21 1 |
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 | ADSC QUANTUM 315 | 2010-01-25 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | NSLS BEAMLINE X25 | 1.0000 | NSLS | X25 |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 1.6 | 50 | 96.9 | 0.06 | 15.8 | 6.2 | 17941 | 17941 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 1.6 | 1.63 | 93.4 | 0.231 | 5.6 |
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 (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 3BDC with all H2Os, Ca2+ and THP removed and the following truncations: H8A, T13A, V23A, Q30A, K64A, T82A, Y113A, V114A, Y115A; all b-factors were reset to 20A2. | 1.6 | 32.05 | 18491 | 16103 | 1808 | 96.85 | 0.17768 | 0.17387 | 0.21263 | RANDOM | 18.234 |
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] | |
-0.79 | 0.8 | -1.78 | 2.7 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 33.04 |
r_dihedral_angle_3_deg | 17.228 |
r_dihedral_angle_4_deg | 9.438 |
r_dihedral_angle_1_deg | 6.336 |
r_scangle_it | 4.751 |
r_scbond_it | 3.217 |
r_mcangle_it | 2.128 |
r_angle_refined_deg | 1.721 |
r_mcbond_it | 1.41 |
r_chiral_restr | 0.147 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 1031 |
Nucleic Acid Atoms | |
Solvent Atoms | 96 |
Heterogen Atoms | 26 |
Software
Software | |
---|---|
Software Name | Purpose |
SCALEPACK | data scaling |
PHASER | phasing |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
CBASS | data collection |
DPS | data reduction |