Lysozyme, 9-11 fs FEL pulses as determined by XTCAV
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 | 4N5R | |
Crystallization
Crystalization Experiments |
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ID | Method | pH | Temperature | Details |
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1 | BATCH MODE | 4 | 293 | 10 % NaCl, 0.1 M sodium acetate buffer, pH 4.0, soaked in 100 mM gadoteridol 30 min. before data collection |
Crystal Properties |
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Matthews coefficient | Solvent content |
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2.05 | 40.03 |
Crystal Data
Unit Cell |
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Length ( Å ) | Angle ( ˚ ) |
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a = 77.75 | α = 90 |
b = 77.75 | β = 90 |
c = 38.9 | γ = 90 |
Symmetry |
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Space Group | P 43 21 2 |
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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 | 293 | PIXEL | CS-PAD CXI-1 | | 2015-02-15 | 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 CXI | 1.393 | SLAC LCLS | CXI |
Serial Crystallography
Sample delivery method |
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Diffraction ID | Description | Sample Delivery Method |
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1 | | injection |
Data Collection
Overall |
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | CC (Half) | 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 | 1.64 | 22.45 | 100 | 0.923 | 0.237 | 3.4 | 1 | | 15159 | | | |
Highest Resolution Shell |
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | CC (Half) | R Split (All) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) |
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1 | 1.64 | 1.68 | | 100 | 0.411 | 0.83 | 1.3 | | |
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 | FOURIER SYNTHESIS | FREE R-VALUE | 4N5R | 1.665 | 22.45 | 15119 | 1512 | 99.697 | 0.205 | 0.2011 | 0.2396 | 18.706 |
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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-0.003 | | | -0.003 | | 0.005 |
RMS Deviations |
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Key | Refinement Restraint Deviation |
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r_dihedral_angle_2_deg | 30.826 |
r_dihedral_angle_4_deg | 21.87 |
r_dihedral_angle_3_deg | 14.639 |
r_dihedral_angle_1_deg | 6.938 |
r_lrange_it | 4.65 |
r_lrange_other | 4.625 |
r_scangle_it | 3.723 |
r_scangle_other | 3.721 |
r_scbond_it | 2.478 |
r_scbond_other | 2.476 |
RMS Deviations |
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Key | Refinement Restraint Deviation |
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r_dihedral_angle_2_deg | 30.826 |
r_dihedral_angle_4_deg | 21.87 |
r_dihedral_angle_3_deg | 14.639 |
r_dihedral_angle_1_deg | 6.938 |
r_lrange_it | 4.65 |
r_lrange_other | 4.625 |
r_scangle_it | 3.723 |
r_scangle_other | 3.721 |
r_scbond_it | 2.478 |
r_scbond_other | 2.476 |
r_mcangle_other | 1.89 |
r_mcangle_it | 1.888 |
r_angle_refined_deg | 1.57 |
r_angle_other_deg | 1.45 |
r_mcbond_it | 1.352 |
r_mcbond_other | 1.288 |
r_nbd_refined | 0.223 |
r_symmetry_nbd_other | 0.2 |
r_nbd_other | 0.191 |
r_xyhbond_nbd_refined | 0.184 |
r_nbtor_refined | 0.168 |
r_symmetry_xyhbond_nbd_refined | 0.133 |
r_symmetry_nbtor_other | 0.092 |
r_chiral_restr | 0.09 |
r_symmetry_nbd_refined | 0.077 |
r_metal_ion_refined | 0.051 |
r_bond_refined_d | 0.009 |
r_gen_planes_refined | 0.008 |
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 | 992 |
Nucleic Acid Atoms | |
Solvent Atoms | 52 |
Heterogen Atoms | 58 |
Software
Software |
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Software Name | Purpose |
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REFMAC | refinement |
CrystFEL | data reduction |
CrystFEL | data scaling |
REFMAC | phasing |