Phycocyanin structure from a modular droplet injector for serial femtosecond crystallography
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 | 7S50 | |
Crystallization
Crystalization Experiments |
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ID | Method | pH | Temperature | Details |
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1 | BATCH MODE | | 277 | 75 mM HEPES pH 7.0, 20 mM MgCl2, 9% PEG 3350 |
Crystal Properties |
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Matthews coefficient | Solvent content |
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2.92 | 57.9 |
Crystal Data
Unit Cell |
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Length ( Å ) | Angle ( ˚ ) |
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a = 188.3 | α = 90 |
b = 188.3 | β = 90 |
c = 61.1 | γ = 120 |
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 | 293 | PIXEL | SLAC ePix10k | | 2021-05-29 | M | SINGLE WAVELENGTH |
Radiation Source |
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
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1 | FREE ELECTRON LASER | SLAC LCLS BEAMLINE MFX | 1.285 | SLAC LCLS | MFX |
Serial Crystallography
Sample delivery method |
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Diffraction ID | Description | Sample Delivery Method |
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1 | Segmnteted Flow | injection |
Measurement |
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Diffraction ID | Pulse Duration | Pulse Repetition Rate | Focal Spot Size | Pulse Energy | Photons Per Pulse |
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1 | 40 (fs) | 120 | | undefined (KeV) | |
Data Reduction |
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Diffraction ID | Frames Indexed | Crystal Hits | Frames Indexed | Latices Merged |
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1 | 5216 | 7465 | 5216 | |
Data Collection
Overall |
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | 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 | 24.6 | 100 | 0.717 | 1.8 | 28 | | 54596 | | | |
Highest Resolution Shell |
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) |
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1 | 2 | 2.1 | | | 0.144 | 0.6 | | |
Refinement
Statistics |
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Diffraction ID | Structure Solution Method | Cross Validation method | 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 |
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X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 2 | 22.31 | 26538 | 1380 | 99.84 | 0.20632 | 0.2043 | 0.24512 | RANDOM | 28.553 |
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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0.65 | 0.33 | | 0.65 | | -2.12 |
RMS Deviations |
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Key | Refinement Restraint Deviation |
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r_dihedral_angle_3_deg | 14.117 |
r_dihedral_angle_1_deg | 5.736 |
r_long_range_B_refined | 5.445 |
r_long_range_B_other | 5.425 |
r_scangle_other | 3.769 |
r_dihedral_angle_2_deg | 3.413 |
r_scbond_it | 2.456 |
r_scbond_other | 2.455 |
r_mcangle_other | 1.935 |
r_mcangle_it | 1.934 |
RMS Deviations |
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Key | Refinement Restraint Deviation |
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r_dihedral_angle_3_deg | 14.117 |
r_dihedral_angle_1_deg | 5.736 |
r_long_range_B_refined | 5.445 |
r_long_range_B_other | 5.425 |
r_scangle_other | 3.769 |
r_dihedral_angle_2_deg | 3.413 |
r_scbond_it | 2.456 |
r_scbond_other | 2.455 |
r_mcangle_other | 1.935 |
r_mcangle_it | 1.934 |
r_mcbond_it | 1.309 |
r_mcbond_other | 1.304 |
r_angle_refined_deg | 1.143 |
r_angle_other_deg | 0.453 |
r_chiral_restr | 0.052 |
r_bond_refined_d | 0.009 |
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 | 2499 |
Nucleic Acid Atoms | |
Solvent Atoms | 126 |
Heterogen Atoms | 130 |
Software
Software |
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Software Name | Purpose |
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REFMAC | refinement |
CrystFEL | data reduction |
Aimless | data scaling |
MOLREP | phasing |