Hen egg-white lysozyme refined against 5000 9 keV diffraction patterns
Serial Crystallography (SX)
Crystallization
Crystalization Experiments |
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ID | Method | pH | Temperature | Details |
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1 | BATCH MODE | | 293 | Sodium chloride |
Crystal Properties |
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Matthews coefficient | Solvent content |
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2.14 | 42.5 |
Crystal Data
Unit Cell |
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Length ( Å ) | Angle ( ˚ ) |
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a = 79.1 | α = 90 |
b = 79.1 | β = 90 |
c = 39.2 | 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 | CCD | MPCCD | | 2016-01-01 | M | MAD |
Radiation Source |
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
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1 | FREE ELECTRON LASER | SACLA BEAMLINE BL3 | 1.38 | SACLA | BL3 |
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 | 1.9 | 57 | 100 | 0.876 | 0.248 | 4.7 | 68 | | 10028 | | | |
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 | 1.9 | 2 | 100 | | 0.867 | | 48 | |
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 (Depositor) | R-Work (DCC) | R-Free (Depositor) | R-Free (DCC) | R-Free Selection Details | Mean Isotropic B |
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X-RAY DIFFRACTION | SAD | THROUGHOUT | 1.9 | 55.93 | 9795 | 477 | 99.94 | 0.18698 | 0.18566 | 0.19 | 0.21435 | 0.22 | RANDOM | 16.675 |
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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0.02 | | | 0.02 | | -0.04 |
RMS Deviations |
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Key | Refinement Restraint Deviation |
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r_dihedral_angle_2_deg | 31.292 |
r_dihedral_angle_4_deg | 17.954 |
r_dihedral_angle_3_deg | 11.357 |
r_dihedral_angle_1_deg | 5.46 |
r_long_range_B_refined | 3.537 |
r_long_range_B_other | 3.38 |
r_angle_refined_deg | 1.659 |
r_scangle_other | 1.161 |
r_angle_other_deg | 0.946 |
r_mcangle_it | 0.928 |
RMS Deviations |
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Key | Refinement Restraint Deviation |
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r_dihedral_angle_2_deg | 31.292 |
r_dihedral_angle_4_deg | 17.954 |
r_dihedral_angle_3_deg | 11.357 |
r_dihedral_angle_1_deg | 5.46 |
r_long_range_B_refined | 3.537 |
r_long_range_B_other | 3.38 |
r_angle_refined_deg | 1.659 |
r_scangle_other | 1.161 |
r_angle_other_deg | 0.946 |
r_mcangle_it | 0.928 |
r_mcangle_other | 0.928 |
r_scbond_it | 0.671 |
r_scbond_other | 0.671 |
r_mcbond_it | 0.536 |
r_mcbond_other | 0.536 |
r_chiral_restr | 0.176 |
r_bond_refined_d | 0.007 |
r_gen_planes_refined | 0.003 |
r_bond_other_d | 0.001 |
r_gen_planes_other | 0.001 |
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 | 992 |
Nucleic Acid Atoms | |
Solvent Atoms | 70 |
Heterogen Atoms | 59 |
Software
Software |
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Software Name | Purpose |
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REFMAC | refinement |
autoSHARP | phasing |