1V0U
Phospholipase D from Streptomyces sp. strain PMF soaked with the product glycerophosphate.
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
---|---|---|---|
Type | Source | Accession Code | Details |
experimental model | PDB | 1F0I | PDB ENTRY 1F0I |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | 5.4 | 0.2 M NH4AC, 0.1 M CITRATE/ PHOSPHATE BUFFER AT PH5.4, 27.5% PEG 4000. CRYSTALS WERE THEREAFTER BACKSOAKED TWICE IN A PHOSPHATE-FREE BUFFER TO REMOVE TRACE-AMOUNTS OF PHOSPHATE., pH 5.40 |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
2 | 38.4 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 57.39 | α = 90 |
b = 57.04 | β = 93.04 |
c = 68.76 | 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 CCD | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID14-4 | ESRF | ID14-4 |
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 | 1.42 | 69.01 | 93.8 | 0.049 | 9.3 | 3.3 | 76771 |
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 | 1.42 | 1.5 | 78.8 | 0.326 | 2 | 2.4 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 1F0I | 1.42 | 69.01 | 76771 | 2408 | 93.8 | 0.167 | 0.166 | 0.186 | RANDOM | 15.12 |
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] | |
-1.05 | -0.44 | 0.67 | 0.34 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_1_deg | 6.619 |
r_scangle_it | 3.34 |
r_scbond_it | 2.107 |
r_angle_refined_deg | 1.814 |
r_mcangle_it | 1.516 |
r_angle_other_deg | 0.905 |
r_mcbond_it | 0.856 |
r_symmetry_vdw_other | 0.267 |
r_nbd_other | 0.249 |
r_nbd_refined | 0.242 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 3692 |
Nucleic Acid Atoms | |
Solvent Atoms | 608 |
Heterogen Atoms | 4 |
Software
Software | |
---|---|
Software Name | Purpose |
REFMAC | refinement |
DENZO | data reduction |
SCALA | data scaling |
CNS | phasing |