2RHD
Crystal structure of Cryptosporidium parvum small GTPase RAB1A
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2F9L | PDB entry 2F9L |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 297 | 0.2M CaCl2, 20% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 297K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.77 | 67.34 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 107.385 | α = 90 |
b = 107.385 | β = 90 |
c = 45.226 | γ = 120 |
Symmetry | |
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Space Group | P 3 2 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 | ADSC QUANTUM 315 | 2007-07-22 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 19-ID | 0.97942 | APS | 19-ID |
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 | 2.06 | 50 | 99.6 | 0.088 | 0.088 | 9.8 | 6 | 18805 | 18805 | 25.8 |
Highest Resolution Shell | |||||||||||||||||||
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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) | ||||||||||
2.06 | 2.13 | 99.5 | 0.321 | 0.321 | 4.92 | 4.7 | 1838 |
Refinement
Statistics | |||||||||||||||||||
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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 | PDB entry 2F9L | 2.06 | 50 | 18186 | 18186 | 601 | 99.41 | 0.18064 | 0.18064 | 0.17969 | 0.2089 | RANDOM | 27.802 |
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] | |
1.01 | 0.51 | 1.01 | -1.52 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 34.525 |
r_dihedral_angle_3_deg | 12.926 |
r_dihedral_angle_4_deg | 10.955 |
r_dihedral_angle_1_deg | 5.462 |
r_scangle_it | 3.104 |
r_scbond_it | 2.054 |
r_mcangle_it | 1.4 |
r_angle_refined_deg | 1.155 |
r_mcbond_it | 0.793 |
r_nbtor_refined | 0.3 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1296 |
Nucleic Acid Atoms | |
Solvent Atoms | 182 |
Heterogen Atoms | 31 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
HKL-3000 | data collection |
HKL-3000 | data reduction |
HKL-3000 | data scaling |
PHASER | phasing |