4I9C
Crystal structure of aspartyl phosphate phosphatase F from B.subtilis in complex with its inhibitory peptide
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 8.5 | 294 | 1M ammonium sulphate, 17% glycerol, 0.1M tris pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
4.85 | 74.62 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 220.791 | α = 90 |
b = 220.791 | β = 90 |
c = 220.791 | γ = 90 |
Symmetry | |
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Space Group | I 41 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 | 80 | PIXEL | DECTRIS PILATUS 6M | Channel-cut Si(111) + KB focusing mirrors | 2012-09-26 | M | SINGLE WAVELENGTH | |||||
2 | 1 | CCD | MARMOSAIC 225 mm CCD | 2010-09-23 |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ALBA BEAMLINE XALOC | 1.07220 | ALBA | XALOC |
2 | SYNCHROTRON | ESRF BEAMLINE BM14 | 1.07131 | ESRF | BM14 |
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 | 3.1 | 49.37 | 100 | 0.097 | 0.095 | 31.3 | 22 | 16988 | 16991 | 1 | 1 | 107.9 |
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 | 3.1 | 3.26 | 100 | 0.265 | 0.265 | 3.3 | 22.3 | 2427 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | 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 | 3.1 | 47.07 | 2 | 16969 | 15637 | 1332 | 99.92 | 0.18962 | 0.18648 | 0.18648 | 0.22686 | RANDOM | 96.074 |
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] | |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 39.226 |
r_dihedral_angle_3_deg | 23.887 |
r_dihedral_angle_4_deg | 18.057 |
r_dihedral_angle_1_deg | 5.744 |
r_angle_refined_deg | 1.711 |
r_chiral_restr | 0.108 |
r_bond_refined_d | 0.015 |
r_gen_planes_refined | 0.009 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3187 |
Nucleic Acid Atoms | |
Solvent Atoms | 18 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
xaloc | data collection |
MOLREP | phasing |
REFMAC | refinement |
XDS | data reduction |
SCALA | data scaling |