1LYC
The impact of the physical and chemical enviroment on the molecular structure of Coprinus cinereus peroxidase
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 4.25 | 293 | 1.5M-1.6M NH4H2PO, pH 4.0-4.5, VAPOR DIFFUSION, HANGING DROP, pH 4.25, temperature 293K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.31 | 46.71 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 77.289 | α = 90 |
b = 115.055 | β = 90 |
c = 36.97 | γ = 90 |
Symmetry | |
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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 | 1998-09-23 | M | SINGLE WAVELENGTH | ||||||
2 | 1 | x-ray | 100 | IMAGE PLATE | RIGAKU RAXIS IIC | 1999-08-27 | M | SINGLE WAVELENGTH | ||||||
3 | 1 | x-ray | 100 | IMAGE PLATE | MARRESEARCH | 2000-02-25 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | EMBL/DESY, HAMBURG BEAMLINE BW7B | 0.8346 | EMBL/DESY, HAMBURG | BW7B |
2 | ROTATING ANODE | RIGAKU | 1.5418 | ||
3 | ROTATING ANODE | RIGAKU | 1.5418 |
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 | |||||||
1,2,3 | 1.57 | 15 | 99 | 0.139 | 0.139 | 47148 | 46580 | -3 | 28.9 |
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) | ||||||||||
1.57 | 1.6 | 96 | 0.223 | 0.223 |
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 | future PDB deposition | 1.57 | 14.89 | 89176 | 46580 | 4227 | 98.3 | 0.225 | 0.223 | 0.223 | 0.265 | RANDOM | 34 |
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] | |
-10.25 | -5.58 | 15.83 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
c_dihedral_angle_d | 22 |
c_angle_deg | 1.5 |
c_mcangle_it | 1.25 |
c_improper_angle_d | 1 |
c_mcbond_it | 0.78 |
c_scangle_it | 0.67 |
c_scbond_it | 0.42 |
c_bond_d | 0.019 |
c_bond_d_na | |
c_bond_d_prot |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4918 |
Nucleic Acid Atoms | |
Solvent Atoms | 342 |
Heterogen Atoms | 90 |
Software
Software | |
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Software Name | Purpose |
DENZO | data reduction |
SCALEPACK | data scaling |
AMoRE | phasing |
CNS | refinement |