2BWQ
Crystal Structure of the RIM2 C2A-domain at 1.4 angstrom Resolution
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1V27 | PDB ENTRY 1V27 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 4.5 | 293 | RAT RIM2 C2A-DOMAIN (RESIDUES 722-859) DISSOLVED IN 20 MM MES (PH 6.0), 150 MM NACL AND 1 MM EDTA WAS CONCENTRATED TO 25 MG/ML AND CRYSTALLIZED IN 17.5% (W/V) PEG 4000, 0.2 M (NH4)2SO4, 0.1M SODIUM ACETATE (PH 4.5) AT 20 DEGREES C USING THE HANGING-DROP VAPOR-DIFFUSION METHOD. CRYSTALS APPEARED OVERNIGHT AND GREW TO A FINAL SIZE OF 0.05 X 0.05 X 0.1 MM WITHIN TWO DAYS. PRIOR TO DATA COLLECTION, CRYSTALS WERE TRANSFERRED INTO A SOLUTION OF 20% (W/V) PEG 4000, 0.15M NACL, 0.2 M (NH4)2SO4, 0.1M SODIUM ACETATE (PH 4.5) AND 15% (V/V) ETHYLENE GLYCOL, AND THEN FLASH-COOLED IN LIQUID PROPANE. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
1.8 | 29.7 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 25.455 | α = 90 |
b = 44.807 | β = 103.86 |
c = 55.756 | γ = 90 |
Symmetry | |
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Space Group | P 1 21 1 |
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 | CUSTOM | 2004-08-13 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 19-ID | APS | 19-ID |
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 | 1.41 | 20.91 | 98.5 | 0.02 | 52.9 | 4 | 23283 | -3 |
Highest Resolution Shell | |||||||||||||||||||
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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 | 1.41 | 1.43 | 82 | 0.18 | 5.2 | 2.8 |
Refinement
Statistics | |||||||||||||||||||
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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 1V27 | 1.41 | 20 | 21884 | 1383 | 99.2 | 0.183 | 0.181 | 0.213 | RANDOM | 17.71 |
Temperature Factor Modeling | ||||||
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Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
0.41 | 0.12 | 0.41 | -0.75 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 34.433 |
r_dihedral_angle_4_deg | 23.439 |
r_dihedral_angle_3_deg | 12.82 |
r_dihedral_angle_1_deg | 6.838 |
r_scangle_it | 4.907 |
r_scbond_it | 3.279 |
r_mcangle_it | 2.147 |
r_angle_refined_deg | 1.914 |
r_mcbond_it | 1.44 |
r_nbtor_refined | 0.321 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1041 |
Nucleic Acid Atoms | |
Solvent Atoms | 110 |
Heterogen Atoms | 10 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
AMoRE | phasing |