4LP9
Endothiapepsin complexed with Phe-reduced-Tyr peptide.
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
---|---|---|---|
Type | Source | Accession Code | Details |
experimental model | PDB | 1GVX | PDB ENTRY 1GVX |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 4.9 | 294 | 0.1 M sodium acetate, 63% saturated ammonium sulfate, 3 mg/ml enzyme, 2 mM inhibitor (dissolved initially in DMSO), pH 4.9, VAPOR DIFFUSION, HANGING DROP, temperature 294.0K |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
2.35 | 47.72 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 52.62 | α = 90 |
b = 72.787 | β = 108.54 |
c = 45.113 | 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 | PIXEL | PSI PILATUS 6M | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I02 | 1.0435 | Diamond | I02 |
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 | 1.35 | 28.32 | 98.2 | 0.047 | 0.047 | 14.8 | 3.3 | 69622 | 69622 | 11.1 |
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 | 1.35 | 1.38 | 84.1 | 0.571 | 0.571 | 2.1 | 2.3 | 4381 |
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 | FOURIER SYNTHESIS | THROUGHOUT | PDB ENTRY 1GVX | 1.35 | 27.72 | 70843 | 66078 | 3576 | 98.42 | 0.1252 | 0.1231 | 0.1649 | RANDOM | 16.182 |
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] | |
0.06 | -0.03 | -0.05 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_sphericity_free | 42.192 |
r_dihedral_angle_2_deg | 30.028 |
r_dihedral_angle_4_deg | 23.079 |
r_sphericity_bonded | 12.406 |
r_dihedral_angle_3_deg | 11.02 |
r_dihedral_angle_1_deg | 6.5 |
r_rigid_bond_restr | 5.698 |
r_long_range_B_refined | 5.363 |
r_long_range_B_other | 5.351 |
r_scangle_other | 4.011 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 2461 |
Nucleic Acid Atoms | |
Solvent Atoms | 335 |
Heterogen Atoms | 51 |
Software
Software | |
---|---|
Software Name | Purpose |
GDA | data collection |
FFT | model building |
REFMAC | refinement |
XDS | data reduction |
SCALA | data scaling |
FFT | phasing |