5MBX
Crystal structure of reduced murine N1-acetylpolyamine oxidase in complex with N1-acetylspermine
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 5LAE |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 8.5 | 293 | PROTEIN AT 23MG/ML IN 20 MM HEPES, PH 7.0, 100 MM NACL, 5% (V/V) GLYCEROL AND 2.5 MM TCEP WAS EQUILIBRATED AGAINST 2.2 M (NH4)2SO4, 0.2 M NASCN, 0.1 M TRIS PH 8. N1-ACETYL SPERMINE WAS SOAKED INTO PRE-FORMED CRYSTAL |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.29 | 46.35 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 121.99 | α = 90 |
b = 121.99 | β = 90 |
c = 54.91 | γ = 120 |
Symmetry | |
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Space Group | P 61 |
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 | PIXEL | DECTRIS PILATUS 6M-F | 2016-10-03 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I04 | 0.975 | Diamond | I04 |
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 | 1.4 | 40.81 | 88.8 | 0.066 | 20.1 | 10.1 | 81328 | 18.4 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 1.4 | 1.48 | 51.5 | 0.417 | 0.908 | 4.5 | 8.4 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | 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 | THROUGHOUT | 5LAE | 1.4 | 40.81 | 80940 | 4187 | 88.2 | 0.181 | 0.18 | 0.2 | RANDOM | 21.77 |
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] | |
-0.2446 | -0.2446 | 0.4892 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
t_other_torsion | 15.5 |
t_omega_torsion | 3.93 |
t_angle_deg | 1.03 |
t_bond_d | 0.01 |
t_dihedral_angle_d | |
t_incorr_chiral_ct | |
t_pseud_angle | |
t_trig_c_planes | |
t_gen_planes | |
t_it |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3672 |
Nucleic Acid Atoms | |
Solvent Atoms | 311 |
Heterogen Atoms | 75 |
Software
Software | |
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Software Name | Purpose |
BUSTER | refinement |
Aimless | data scaling |
XDS | data reduction |
MOLREP | phasing |