2ZE9
Crystal structure of H168A mutant of phospholipase D from Streptomyces antibioticus, as a complex with phosphatidylcholine
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
---|---|---|---|
Type | Source | Accession Code | Details |
experimental model | PDB | 2ZE4 | PDB ENTRY 2ZE4 |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6 | 291 | 15% PEG 6000, 0.1M MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
2.17 | 43.45 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 60.868 | α = 90 |
b = 78.232 | β = 90 |
c = 98.603 | γ = 90 |
Symmetry | |
---|---|
Space Group | P 21 21 21 |
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 | RIGAKU RAXIS IV | mirrors | 1999-07-01 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU RU300 | 1.5418 |
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 | 2.3 | 61.31 | 97 | 0.07 | 17.2 | 3.4 | 21448 | 20805 | 23.6 |
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) | |||||||||||
2.3 | 2.42 | 88.8 | 0.157 | 5.5 | 2.2 | 2726 |
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 2ZE4 | 2.3 | 48.04 | 21555 | 19582 | 1071 | 95.84 | 0.17448 | 0.17448 | 0.17029 | 0.25137 | RANDOM | 13.618 |
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] | |
-0.21 | 0.5 | -0.29 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 38.105 |
r_dihedral_angle_4_deg | 22.262 |
r_dihedral_angle_3_deg | 15.629 |
r_dihedral_angle_1_deg | 8.218 |
r_scangle_it | 3.584 |
r_scbond_it | 2.329 |
r_angle_refined_deg | 1.894 |
r_mcangle_it | 1.512 |
r_mcbond_it | 0.928 |
r_nbtor_refined | 0.301 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 3758 |
Nucleic Acid Atoms | |
Solvent Atoms | 365 |
Heterogen Atoms | 38 |
Software
Software | |
---|---|
Software Name | Purpose |
REFMAC | refinement |
CrystalClear | data collection |
DENZO | data reduction |
SCALA | data scaling |
MOLREP | phasing |