High-viscosity injector-based Pink Beam Serial Crystallography of Micro-crystals at a Synchrotron Radiation Source
Serial Crystallography (SX)
Starting Model(s)
Initial Refinement Model(s) |
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Type | Source | Accession Code | Details |
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experimental model | PDB | 5UVI | |
Crystallization
Crystalization Experiments |
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ID | Method | pH | Temperature | Details |
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1 | LIPIDIC CUBIC PHASE | 5 | 298 | sodium citrate pH 5.0, PEG 400, sodium thiocyanate |
Crystal Properties |
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Matthews coefficient | Solvent content |
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2.54 | 51.63 |
Crystal Data
Unit Cell |
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Length ( Å ) | Angle ( ˚ ) |
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a = 40 | α = 90 |
b = 179 | β = 90 |
c = 142 | γ = 90 |
Symmetry |
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Space Group | C 2 2 21 |
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Diffraction
Diffraction Experiment |
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ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol |
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1 | 1 | x-ray | 298 | CCD | RAYONIX MX340-HS | | 2017-06-24 | L | LAUE |
Radiation Source |
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
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1 | SYNCHROTRON | APS BEAMLINE 14-ID-B | 1.033-1.67 | APS | 14-ID-B |
Data Collection
Overall |
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Split (All) | 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 |
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1 | 4.2 | 50 | 87.8 | 0.27 | 4.5 | 11.5 | | 4021 | | | |
Highest Resolution Shell |
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Split (All) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) |
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1 | 4.2 | 4.3 | | | 0.262 | | | |
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 (Depositor) | R-Work (DCC) | R-Free (Depositor) | R-Free (DCC) | R-Free Selection Details | Mean Isotropic B |
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X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 5UVI | 4.2 | 50 | 3179 | 353 | 87.77 | 0.25385 | 0.24997 | 0.25 | 0.28767 | 0.28 | RANDOM | 58.074 |
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] |
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-0.74 | | | 0.82 | | -0.08 |
RMS Deviations |
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Key | Refinement Restraint Deviation |
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r_dihedral_angle_2_deg | 39.518 |
r_dihedral_angle_4_deg | 15.128 |
r_long_range_B_refined | 11.522 |
r_long_range_B_other | 11.522 |
r_dihedral_angle_3_deg | 11.458 |
r_mcangle_other | 4.223 |
r_mcangle_it | 4.222 |
r_dihedral_angle_1_deg | 4.073 |
r_scangle_other | 3.47 |
r_mcbond_it | 2.402 |
RMS Deviations |
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Key | Refinement Restraint Deviation |
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r_dihedral_angle_2_deg | 39.518 |
r_dihedral_angle_4_deg | 15.128 |
r_long_range_B_refined | 11.522 |
r_long_range_B_other | 11.522 |
r_dihedral_angle_3_deg | 11.458 |
r_mcangle_other | 4.223 |
r_mcangle_it | 4.222 |
r_dihedral_angle_1_deg | 4.073 |
r_scangle_other | 3.47 |
r_mcbond_it | 2.402 |
r_mcbond_other | 2.382 |
r_scbond_it | 1.853 |
r_scbond_other | 1.852 |
r_angle_refined_deg | 1.043 |
r_angle_other_deg | 0.861 |
r_chiral_restr | 0.045 |
r_bond_refined_d | 0.006 |
r_gen_planes_refined | 0.004 |
r_bond_other_d | 0.002 |
r_gen_planes_other | 0.002 |
r_nbd_refined | |
r_nbd_other | |
r_nbtor_refined | |
r_nbtor_other | |
r_xyhbond_nbd_refined | |
r_xyhbond_nbd_other | |
r_metal_ion_refined | |
r_metal_ion_other | |
r_symmetry_vdw_refined | |
r_symmetry_vdw_other | |
r_symmetry_hbond_refined | |
r_symmetry_hbond_other | |
r_symmetry_metal_ion_refined | |
r_symmetry_metal_ion_other | |
r_scangle_it | |
r_rigid_bond_restr | |
r_sphericity_free | |
r_sphericity_bonded | |
Non-Hydrogen Atoms Used in Refinement |
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Non-Hydrogen Atoms | Number |
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Protein Atoms | 2978 |
Nucleic Acid Atoms | |
Solvent Atoms | |
Heterogen Atoms | 25 |
Software
Software |
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Software Name | Purpose |
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REFMAC | refinement |
CrystFEL | data reduction |
PHASER | phasing |