4F1J
Crystal structure of the MG2+ loaded VWA domain of plasmodium falciparum trap protein
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 5.5 | 293 | 25% PEG 3350, 0.1M BIS-TRIS, 0.2M MAGNESIUM SULFATE, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.28 | 46.09 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 89.313 | α = 90 |
b = 89.313 | β = 90 |
c = 104.192 | γ = 90 |
Symmetry | |
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Space Group | P 43 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 | 100 | CCD | MARMOSAIC 225 mm CCD | THE OPTICAL ELEMENTS CONSIST OF A VERTICALLY COLLIMATING MIRROR (M1, FOCUS AT INFINITY) FOLLOWED BY A BARTELS MONOCHROMATOR WITH DUAL CHANNEL CUT CRYSTALS (DCCM) IN (+--+) GEOMETRY, AND A TOROIDAL MIRROR (M2) TO VERTICALLY AND HORIZONTALLY FOCUS THE BEAM AT THE SAMPLE POSITION (WITH 2:1 HORIZONTAL DEMAGNIFICATION) | 2010-05-24 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SLS BEAMLINE X06DA | 1.0 | SLS | X06DA |
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 | 1.73 | 50 | 99.8 | 0.13 | 14.72 | 10.271 | 84445 | -3 | -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 | 1.73 | 1.83 | 98.6 | 0.853 | 2.9 | 10 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | 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 | SIRAS | THROUGHOUT | 1.73 | 30 | 44675 | 42440 | 2235 | 100 | 0.17905 | 0.17905 | 0.177 | 0.21819 | RANDOM | 11.147 |
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] | |
0.07 | 0.07 | -0.14 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 37.355 |
r_dihedral_angle_3_deg | 11.893 |
r_dihedral_angle_4_deg | 8.109 |
r_dihedral_angle_1_deg | 6.106 |
r_scangle_it | 3.208 |
r_scbond_it | 2.196 |
r_angle_refined_deg | 1.399 |
r_mcangle_it | 1.246 |
r_angle_other_deg | 0.932 |
r_mcbond_it | 0.921 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3088 |
Nucleic Acid Atoms | |
Solvent Atoms | 391 |
Heterogen Atoms | 89 |
Software
Software | |
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Software Name | Purpose |
MAR345dtb | data collection |
SHARP | phasing |
REFMAC | refinement |
XDS | data reduction |
XDS | data scaling |