4HXE
Pyrococcus horikoshii acylaminoacyl peptidase (uncomplexed)
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 8.5 | 298 | 3.0 M 1,6-hexanediol, 0.20 M MgCl2, 0.1 M Tris/HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.18 | 61.29 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 183 | α = 90 |
b = 183 | β = 90 |
c = 144.63 | γ = 120 |
Symmetry | |
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Space Group | H 3 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 | IMAGE PLATE | RIGAKU RAXIS IIC | 2005-06-17 | M | SINGLE WAVELENGTH | ||||||
2 | 1 | x-ray | 100 | IMAGE PLATE | RIGAKU RAXIS IIC | 2006-03-23 | M | SINGLE WAVELENGTH | ||||||
3 | 1 | x-ray | 100 | IMAGE PLATE | RIGAKU RAXIS IIC | 2006-03-03 | M | SINGLE WAVELENGTH | ||||||
4 | 1 | x-ray | 100 | CCD | MAR CCD 165 mm | mirrors | 2006-06-29 | M | MAD | |||||
5 | 1 | x-ray | 100 | CCD | MARMOSAIC 225 mm CCD | mirrors | 2006-06-29 | M | MAD |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU RU200 | 1.5418 | ||
2 | ROTATING ANODE | RIGAKU RU200 | 1.5418 | ||
3 | ROTATING ANODE | RIGAKU RU200 | 1.5418 | ||
4 | SYNCHROTRON | EMBL/DESY, HAMBURG BEAMLINE X11 | 0.8162 | EMBL/DESY, HAMBURG | X11 |
5 | SYNCHROTRON | ESRF BEAMLINE BM14 | 1.0715 | ESRF | BM14 |
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 | ||||||||
1,2,3,4 | 1.9 | 20 | 95.7 | 0.158 | 12.79 | 8.32 | 69738 | 69738 | -3 | 20.794 |
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) | |||||||||||
1,2,3,4 | 1.9 | 2 | 74.6 | 0.686 | 1.87 | 2.84 | 7680 |
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 | MIRAS | THROUGHOUT | 1.91 | 19.78 | 64801 | 64801 | 3425 | 95.16 | 0.1741 | 0.1741 | 0.17219 | 0.21021 | RANDOM | 21.562 |
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] | |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 36.397 |
r_dihedral_angle_4_deg | 19.616 |
r_dihedral_angle_3_deg | 15.731 |
r_dihedral_angle_1_deg | 7.388 |
r_angle_refined_deg | 1.944 |
r_chiral_restr | 0.155 |
r_bond_refined_d | 0.018 |
r_gen_planes_refined | 0.01 |
r_bond_other_d | |
r_angle_other_deg |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4959 |
Nucleic Acid Atoms | |
Solvent Atoms | 395 |
Heterogen Atoms | 51 |
Software
Software | |
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Software Name | Purpose |
bioteX | data collection |
SHELX | model building |
MLPHARE | phasing |
REFMAC | refinement |
XDS | data reduction |
XSCALE | data scaling |
SHELX | phasing |