6YVL
Human OMPD-domain of UMPS in complex with the substrate OMP at 1.25 Angstroms resolution, 1.42 MGy exposure
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2QCD |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 293 | Crystallization: 100 mM Tris/HCl pH 8.0, 1.9 - 2.1 M Ammonium sulfate, 10 mM Glutathion, 5% (v/v) Glycerol Soaking: 100 mM Tris/HCl pH 8.0, 2.0 M Ammonium sulfate, 10 mM Glutathion, 5% (v/v) Glycerol, 50 mM OMP Cryo-protection: 100 mM Tris/HCl pH 8.0, 2.0 M Ammonium sulfate, 10 mM Glutathion, 5% (v/v) Glycerol, 50 mM OMP |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.47 | 50.13 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 77.31 | α = 90 |
b = 116.85 | β = 90 |
c = 61.97 | γ = 90 |
Symmetry | |
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Space Group | C 2 2 21 |
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 EIGER X 16M | 2018-07-08 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2) | 0.82660 | PETRA III, EMBL c/o DESY | P14 (MX2) |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | CC (Half) | 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 | 1.25 | 19.68 | 99.8 | 0.08 | 0.087 | 1 | 15.74 | 6.818 | 77540 | 17.875 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||
1 | 1.25 | 1.3 | 99.9 | 1.382 | 1.496 | 0.662 | 1.69 | 6.837 |
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 | 2QCD | 1.25 | 19.68 | 73773 | 3767 | 99.78 | 0.1302 | 0.1288 | 0.1576 | RANDOM | 15.226 |
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] | |
0.82 | -0.42 | -0.4 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 32.147 |
r_dihedral_angle_4_deg | 16.691 |
r_dihedral_angle_3_deg | 12.509 |
r_rigid_bond_restr | 9.253 |
r_dihedral_angle_1_deg | 6.699 |
r_angle_other_deg | 2.263 |
r_angle_refined_deg | 1.461 |
r_chiral_restr | 0.084 |
r_bond_other_d | 0.035 |
r_gen_planes_other | 0.014 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1962 |
Nucleic Acid Atoms | |
Solvent Atoms | 331 |
Heterogen Atoms | 36 |
Software
Software | |
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Software Name | Purpose |
XDS | data reduction |
XSCALE | data scaling |
MOLREP | phasing |
REFMAC | refinement |
PDB_EXTRACT | data extraction |