1AM5
THE CRYSTAL STRUCTURE AND PROPOSED AMINO ACID SEQUENCE OF A PEPSIN FROM ATLANTIC COD (GADUS MORHUA)
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 5PEP | PDB ENTRY 5PEP |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | 5.4 | 7.5 % 2-PROPANOL, 100 MM SODIUM ACETATE PH 5.4 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.15 | 43 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 35.98 | α = 90 |
b = 75.4 | β = 90 |
c = 108.1 | 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 | 291 | DIFFRACTOMETER | ENRAF-NONIUS FAST | COLLIMATOR | 1995-10-16 | M |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | BRUKER NONIUS |
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 | 2.16 | 20 | 83.7 | 0.066 | 10.8 | 2.7 | 13687 | 1 | 22.3 |
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) | |||||||||||
2.16 | 2.28 | 41.4 | 0.221 | 3.5 | 1.4 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | PDB ENTRY 5PEP | 2.16 | 8 | 3 | 13315 | 0.208 | 0.224 | RANDOM | 17.22 |
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 |
p_chiral_restr | 0.196 |
p_planar_d | 0.091 |
p_angle_d | 0.071 |
p_bond_d | 0.02 |
p_angle_deg | |
p_hb_or_metal_coord | |
p_mcbond_it | |
p_mcangle_it | |
p_scbond_it | |
p_scangle_it |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 2395 |
Nucleic Acid Atoms | |
Solvent Atoms | 161 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
MADNES | data collection |
CCP4 | data reduction |
X-PLOR | model building |
PROLSQ | refinement |
X-PLOR | refinement |
MADNES | data reduction |
CCP4 | data scaling |
X-PLOR | phasing |