Engineered tryptophan synthase b-subunit from Pyrococcus furiosus, PfTrpB2B9-H275E with L-Trp non-covalently bound
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 | 6AM8 | |
Crystallization
Crystalization Experiments |
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ID | Method | pH | Temperature | Details |
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1 | VAPOR DIFFUSION, SITTING DROP | 7.85 | 298 | 13-21% PEG3350, 0.1 M HEPES pH 7.85 |
Crystal Properties |
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Matthews coefficient | Solvent content |
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2.26 | 45.59 |
Crystal Data
Unit Cell |
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Length ( Å ) | Angle ( ˚ ) |
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a = 57.402 | α = 90 |
b = 82.658 | β = 90 |
c = 322.255 | γ = 90 |
Symmetry |
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Space Group | P 21 21 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 | 100 | PIXEL | DECTRIS EIGER X 9M | | 2021-03-28 | M | SINGLE WAVELENGTH |
Radiation Source |
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
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1 | SYNCHROTRON | APS BEAMLINE 21-ID-D | 1.033167 | APS | 21-ID-D |
Serial Crystallography
Sample delivery method |
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Diffraction ID | Description | Sample Delivery Method |
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1 | | fixed target |
Data Collection
Overall |
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | Rpim 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 |
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1 | 2.39 | 50 | 99.5 | 0.058 | 0.998 | 8.4 | 13.4 | | 823988 | | | |
Highest Resolution Shell |
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) |
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1 | 2.39 | 2.45 | 99.5 | | 1.548 | 0.488 | 0.8 | 14.1 | |
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 (All) | R-Work | R-Free | Mean Isotropic B |
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X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 6AM8 | 2.39 | 46.695 | 61584 | 3098 | 99.305 | 0.229 | 0.2272 | 0.2714 | 72.415 |
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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1.735 | | | 5.909 | | -7.644 |
RMS Deviations |
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Key | Refinement Restraint Deviation |
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r_dihedral_angle_2_deg | 33.18 |
r_dihedral_angle_4_deg | 16.624 |
r_dihedral_angle_3_deg | 13.577 |
r_dihedral_angle_1_deg | 6.822 |
r_lrange_it | 2.913 |
r_lrange_other | 2.913 |
r_mcangle_it | 1.293 |
r_mcangle_other | 1.293 |
r_angle_refined_deg | 1.215 |
r_scangle_it | 1.189 |
RMS Deviations |
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Key | Refinement Restraint Deviation |
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r_dihedral_angle_2_deg | 33.18 |
r_dihedral_angle_4_deg | 16.624 |
r_dihedral_angle_3_deg | 13.577 |
r_dihedral_angle_1_deg | 6.822 |
r_lrange_it | 2.913 |
r_lrange_other | 2.913 |
r_mcangle_it | 1.293 |
r_mcangle_other | 1.293 |
r_angle_refined_deg | 1.215 |
r_scangle_it | 1.189 |
r_scangle_other | 1.189 |
r_angle_other_deg | 1.165 |
r_mcbond_it | 0.746 |
r_mcbond_other | 0.746 |
r_scbond_it | 0.69 |
r_scbond_other | 0.69 |
r_symmetry_xyhbond_nbd_refined | 0.216 |
r_symmetry_nbd_refined | 0.205 |
r_nbd_other | 0.203 |
r_nbd_refined | 0.176 |
r_symmetry_nbd_other | 0.173 |
r_nbtor_refined | 0.152 |
r_xyhbond_nbd_refined | 0.15 |
r_symmetry_nbtor_other | 0.074 |
r_chiral_restr | 0.04 |
r_bond_refined_d | 0.004 |
r_gen_planes_refined | 0.004 |
r_bond_other_d | 0.001 |
r_gen_planes_other | 0.001 |
Non-Hydrogen Atoms Used in Refinement |
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Non-Hydrogen Atoms | Number |
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Protein Atoms | 11078 |
Nucleic Acid Atoms | |
Solvent Atoms | 9 |
Heterogen Atoms | 34 |
Software
Software |
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Software Name | Purpose |
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REFMAC | refinement |
XDS | data reduction |
Aimless | data scaling |
PHASER | phasing |