1S3P
Crystal structure of rat alpha-parvalbumin S55D/E59D mutant
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1RTP |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION | VAPOR DIFFUSION |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.06 | 40.3 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 61.47 | α = 90 |
b = 51.57 | β = 90 |
c = 30.75 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 2 |
Diffraction
Diffraction Experiment | ||||||||||||||
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ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 173 | IMAGE PLATE | RIGAKU RAXIS IV | osmic confocal | 2002-12-01 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU | 1.5418 |
Data Collection
Overall | |||||||||||||||||||
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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 | 26 | 99 | 0.055 | 0.055 | 15 | 6 | 7025 | 6942 | 14.5 |
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) | ||||||||||
2 | 2.07 | 98 | 0.14 | 0.14 | 6 | 3 | 1236 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | 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 | 1rtp | 2 | 26.4 | 6942 | 681 | 98.9 | 0.185 | 0.181 | 0.181 | 0.221 | RANDOM | 18.8 |
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] | |
-2.5 | 3.46 | -0.96 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
c_dihedral_angle_d | 20.5 |
c_scangle_it | 2.91 |
c_scbond_it | 2.04 |
c_mcangle_it | 1.9 |
c_angle_deg | 1.5 |
c_mcbond_it | 1.31 |
c_improper_angle_d | 0.89 |
c_bond_d | 0.009 |
c_bond_d_na | |
c_bond_d_prot |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 829 |
Nucleic Acid Atoms | |
Solvent Atoms | 129 |
Heterogen Atoms | 7 |
Software
Software | |
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Software Name | Purpose |
CNS | refinement |
SCALEPACK | data scaling |
MOLREP | phasing |