2OXR
PAB0955 crystal structure : a GTPase in GDP and Mg bound form from Pyrococcus abyssi (after GTP hydrolysis)
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 5.6 | 293 | 0.1M tri-Na citrate pH 5.6, 15% PEG 4000, 0.2M ammonium acetate, 20mM DTT, 0.65mM GTP, 8mg/ml protein, VAPOR DIFFUSION, HANGING DROP, temperature 293K, pH 5.60 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.19 | 38.7314 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 60.189 | α = 90 |
b = 60.189 | β = 90 |
c = 116.512 | 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 | MAR CCD 130 mm | MIRROR | 2004-02-26 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE BM30A | ESRF | BM30A |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 2.4 | 100 | 99 | 0.067 | 19.55 | 9.3 | 9973 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 2.4 | 2.45 | 98.8 | 0.404 | 0.404 | 5.76 | 9.5 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (All) | 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 | 1YRB | 2.4 | 15 | 10300 | 9913 | 981 | 99.23 | 0.221 | 0.212 | 0.324 | RANDOM | 50.15 |
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] | |
2.39 | 1.19 | 2.39 | -3.58 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 37.452 |
r_dihedral_angle_4_deg | 20.114 |
r_dihedral_angle_3_deg | 18.699 |
r_dihedral_angle_1_deg | 5.467 |
r_scangle_it | 1.744 |
r_mcangle_it | 1.685 |
r_scbond_it | 1.22 |
r_angle_refined_deg | 1.19 |
r_mcbond_it | 0.96 |
r_symmetry_hbond_refined | 0.377 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2001 |
Nucleic Acid Atoms | |
Solvent Atoms | 56 |
Heterogen Atoms | 29 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
XDS | data reduction |
XDS | data scaling |
AMoRE | phasing |