1XRY
Crystal structure of Aeromonas proteolytica aminopeptidase in complex with bestatin
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
---|---|---|---|
Type | Source | Accession Code | Details |
experimental model | PDB | 1AMP | PDB ENTRY 1AMP |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7 | 293 | NaCl, KSCN, HEPES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
2.66 | 53 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 107.39 | α = 90 |
b = 107.39 | β = 90 |
c = 103.06 | γ = 120 |
Symmetry | |
---|---|
Space Group | P 61 2 2 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 293 | AREA DETECTOR | XENTRONICS | 1992-12-14 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | SIEMENS | 1.5418 |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 2.1 | 29.7 | 99.1 | 0.064 | 31.1 | 15.6 | 20836 | 20836 | 19.2 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
2.1 | 2.2 | 94.7 | 0.339 | 2519 |
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 1AMP | 2.1 | 29.69 | 20680 | 20680 | 2041 | 98.2 | 0.168 | 0.168 | 0.164 | 0.197 | RANDOM | 23.9 |
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] | |
-0.02 | 2.86 | -0.02 | 0.04 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
c_dihedral_angle_d | 22.9 |
c_scangle_it | 3.7 |
c_scbond_it | 2.63 |
c_mcangle_it | 2.45 |
c_mcbond_it | 1.64 |
c_angle_deg | 1.2 |
c_improper_angle_d | 0.8 |
c_bond_d | 0.006 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 2210 |
Nucleic Acid Atoms | |
Solvent Atoms | 172 |
Heterogen Atoms | 24 |
Software
Software | |
---|---|
Software Name | Purpose |
CNX | refinement |
X-GEN | data reduction |
XDS | data scaling |
X-PLOR | phasing |