1A0J
CRYSTAL STRUCTURE OF A NON-PSYCHROPHILIC TRYPSIN FROM A COLD-ADAPTED FISH SPECIES.
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
---|---|---|---|
Type | Source | Accession Code | Details |
experimental model | PDB | 3PTB | PDB ENTRY 3PTB BOVINE TRYPSIN, WITH CORRECT AMINO ACID SEQUENCE SUPERIMPOSED ONTO ANIONIC SALMON TRYPSIN 2TBS. |
experimental model | PDB | 2TBS | PDB ENTRY 3PTB BOVINE TRYPSIN, WITH CORRECT AMINO ACID SEQUENCE SUPERIMPOSED ONTO ANIONIC SALMON TRYPSIN 2TBS. |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | 4.6 | pH 4.6 |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
2.2 | 44 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 65.907 | α = 90 |
b = 83.107 | β = 90 |
c = 154.787 | γ = 90 |
Symmetry | |
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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 | 295 | IMAGE PLATE | MARRESEARCH | 1996-08-16 | M |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE BM1A | ESRF | BM1A |
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 | 1.7 | 28 | 81.2 | 0.123 | 3.6 | 5.9 | 76357 | 1 | 19.6 |
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) | |||||||||||
1 | 1.7 | 1.79 | 52.3 | 0.258 | 2.9 | 2 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | 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 3PTB BOVINE TRYPSIN, WITH CORRECT AMINO ACID SEQUENCE SUPERIMPOSED ONTO ANIONIC SALMON TRYPSIN 2TBS. | 1.7 | 8 | 3 | 68062 | 3866 | 73.061 | 0.173 | 0.173 | 0.215 | RANDOM | 22.93 |
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] | |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
x_dihedral_angle_d | 26.35 |
x_angle_deg | 2.697 |
x_improper_angle_d | 1.087 |
x_bond_d | 0.013 |
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 | 6640 |
Nucleic Acid Atoms | |
Solvent Atoms | 379 |
Heterogen Atoms | 87 |
Software
Software | |
---|---|
Software Name | Purpose |
DENZO | data reduction |
XDS | data scaling |
SCALA | data scaling |
Agrovata | data reduction |
CCP4 | data reduction |
AMoRE | phasing |
X-PLOR | refinement |
XDS | data reduction |
CCP4 | data scaling |