1PKL
THE STRUCTURE OF LEISHMANIA PYRUVATE KINASE
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
---|---|---|---|
Type | Source | Accession Code | Details |
experimental model | PDB | 1PKY | PDB ENTRY 1PKY |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | 4.8 | 6% PEG 4000, 20MM AMMONIUM SULPHATE, 15% GLYCEROL, 20MM SODIUM ACETATE PH 4.8 |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
3.33 | 62.8 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 121.649 | α = 90 |
b = 132.638 | β = 97.11 |
c = 180.996 | 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 | IMAGE PLATE | MARRESEARCH | BENT FUSED QUARTZ SINGLE SEGMENT MIRROR | 1997-12-15 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SRS BEAMLINE PX7.2 | SRS | PX7.2 |
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 | 2.35 | 30 | 68 | 0.089 | 5.4 | 1.5 | 160789 |
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 | 2.35 | 2.48 | 47.4 | 0.308 | 2.4 | 1.2 |
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 | OTHER | THROUGHOUT | PDB ENTRY 1PKY | 2.35 | 30 | 160789 | 8074 | 67.9 | 0.209 | 0.209 | 0.256 | RANDOM | 48.9 |
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] | |
-12.518 | -4.1509 | 11.1994 | 1.3186 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
x_dihedral_angle_d | 24 |
x_angle_deg | 1.4 |
x_improper_angle_d | 1.2 |
x_bond_d | 0.009 |
x_bond_d_na | |
x_bond_d_prot | |
x_angle_d | |
x_angle_d_na | |
x_angle_d_prot | |
x_angle_deg_na |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 29994 |
Nucleic Acid Atoms | |
Solvent Atoms | 2952 |
Heterogen Atoms | 40 |
Software
Software | |
---|---|
Software Name | Purpose |
AMoRE | phasing |
FFT | model building |
SHELXS | phasing |
MLPHARE | phasing |
DM | model building |
X-PLOR | refinement |
DENZO | data reduction |
CCP4 | data scaling |
FFT | phasing |
DM | phasing |