1YR7
PAB0955 crystal structure : a GTPase in GTP-gamma-S bound form from Pyrococcus abyssi
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 5.6 | 291 | 13% PEG 4000, 0.2M ammonium acetate, 0.1M tri-sodium citrate dihydrate, 20mM DTT, 0.65mM GTP-gamma-S, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2 | 38.5 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 60.17 | α = 90 |
b = 60.17 | β = 90 |
c = 115.89 | γ = 120 |
Symmetry | |
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Space Group | P 32 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 | MARRESEARCH | mirror | 2004-06-18 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE BM30A | 0.979 | ESRF | BM30A |
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 | 2.08 | 50 | 94.6 | 0.069 | 0.069 | 17.75 | 6.5 | 15141 | 15034 | 45 |
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) | ||||||||||
1 | 2.08 | 2.15 | 64.2 | 0.232 | 0.232 | 6.36 | 4.7 | 893 |
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 | 1YR6 | 2.08 | 15 | 13196 | 12488 | 1587 | 83.18 | 0.21691 | 0.21691 | 0.20835 | 0.29463 | RANDOM | 45.443 |
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] | |
1.8 | 0.9 | 1.8 | -2.7 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 38.069 |
r_dihedral_angle_3_deg | 18.189 |
r_dihedral_angle_4_deg | 17.661 |
r_dihedral_angle_1_deg | 5.595 |
r_scangle_it | 1.921 |
r_mcangle_it | 1.809 |
r_scbond_it | 1.429 |
r_angle_refined_deg | 1.296 |
r_mcbond_it | 1.084 |
r_symmetry_hbond_refined | 0.411 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1981 |
Nucleic Acid Atoms | |
Solvent Atoms | 86 |
Heterogen Atoms | 32 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
ProDC | data collection |
XDS | data scaling |
AMoRE | phasing |