2VK3
Crystal structure of rat profilin 2a
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2V8F | PDB ENTRY 2V8F |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 4.5 | 2M AMMONIUM SULPHATE, 1M NACL, PH 4.5 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.9 | 58 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 51.1 | ¦Á = 90 |
b = 51.1 | ¦Â = 90 |
c = 67.52 | ¦Ã = 90 |
Symmetry | |
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Space Group | P 41 |
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 | 100 | CCD | MARRESEARCH | 2007-11-02 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | EMBL/DESY, HAMBURG BEAMLINE BW7A | EMBL/DESY, HAMBURG | BW7A |
Data Collection
Overall | |||||||||||||||||||
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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 | 20 | 99 | 0.07 | 12.7 | 3.1 | 18939 | -3 | 24 |
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 | 1.74 | 99.8 | 0.52 | 2.2 | 3.1 |
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 (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB ENTRY 2V8F | 1.7 | 17.45 | 17987 | 946 | 99 | 0.175 | 0.173 | 0.216 | RANDOM | 17.47 |
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] | |
-0.01 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 37.112 |
r_dihedral_angle_4_deg | 24.378 |
r_dihedral_angle_3_deg | 14.35 |
r_scangle_it | 7.733 |
r_dihedral_angle_1_deg | 7.687 |
r_scbond_it | 5.884 |
r_mcangle_it | 3.217 |
r_mcbond_it | 2.487 |
r_angle_refined_deg | 1.838 |
r_angle_other_deg | 1.095 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1058 |
Nucleic Acid Atoms | |
Solvent Atoms | 220 |
Heterogen Atoms | 33 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
XSCALE | data scaling |
MOLREP | phasing |