From macrocrystals to microcrystals: a strategy for membrane protein serial crystallography
Serial Crystallography (SX)
Starting Model(s)
Initial Refinement Model(s) |
---|
Type | Source | Accession Code | Details |
---|
|
experimental model | PDB | 2I5N | |
Crystallization
Crystalization Experiments |
---|
ID | Method | pH | Temperature | Details |
---|
1 | VAPOR DIFFUSION, SITTING DROP | 6.8 | 277 | Macrocrystal growth:
10 mg/ml protein
3.6 M ammonium sulphate, 6 % w/v heptane-1,2,3-triol, 20 mM KH203/K2H03 pH 6.8, 0.1 % LDAO
20 ul sitting drop, 10 protein : 10 precipitant
Microcrystals
8.5 mg/ml protein
18.5 ul sitting drop, 10 protein : 7.5 precipitant : 1 seed stock |
Crystal Data
Unit Cell |
---|
Length ( Å ) | Angle ( ˚ ) |
---|
a = 226.5 | α = 90 |
b = 226.5 | β = 90 |
c = 113.9 | γ = 90 |
Symmetry |
---|
Space Group | P 43 21 2 |
---|
Diffraction
Diffraction Experiment |
---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol |
---|
1 | 1 | x-ray | 298 | PIXEL | CS-PAD CXI-1 | | 2016-06-09 | M | SINGLE WAVELENGTH |
Radiation Source |
---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
---|
1 | FREE ELECTRON LASER | SLAC LCLS BEAMLINE CXI | 1.307 | SLAC LCLS | CXI |
Data Collection
Overall |
---|
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 |
---|
1 | 2.4 | 35.7 | 100 | 0.997 | 0.0486 | 11.2 | 1529 | | 118454 | | | |
Highest Resolution Shell |
---|
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) |
---|
1 | 2.4 | 2.46 | 100 | | 0.438 | 1.06 | | 106 | |
Refinement
Statistics |
---|
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 | R-Free | R-Free Selection Details | Mean Isotropic B |
---|
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 2I5N | 2.4 | 35.7 | 109673 | 5711 | 99.95 | 0.16214 | 0.16086 | 0.18632 | RANDOM | 81.496 |
Temperature Factor Modeling |
---|
Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] |
---|
1.21 | | | 1.21 | | -2.42 |
RMS Deviations |
---|
Key | Refinement Restraint Deviation |
---|
r_dihedral_angle_2_deg | 32.56 |
r_dihedral_angle_4_deg | 14.767 |
r_dihedral_angle_3_deg | 13.641 |
r_long_range_B_refined | 7.989 |
r_long_range_B_other | 7.989 |
r_scangle_other | 6.065 |
r_dihedral_angle_1_deg | 5.749 |
r_mcangle_other | 5.29 |
r_mcangle_it | 5.289 |
r_scbond_it | 3.921 |
RMS Deviations |
---|
Key | Refinement Restraint Deviation |
---|
r_dihedral_angle_2_deg | 32.56 |
r_dihedral_angle_4_deg | 14.767 |
r_dihedral_angle_3_deg | 13.641 |
r_long_range_B_refined | 7.989 |
r_long_range_B_other | 7.989 |
r_scangle_other | 6.065 |
r_dihedral_angle_1_deg | 5.749 |
r_mcangle_other | 5.29 |
r_mcangle_it | 5.289 |
r_scbond_it | 3.921 |
r_scbond_other | 3.921 |
r_mcbond_it | 3.547 |
r_mcbond_other | 3.543 |
r_angle_refined_deg | 1.96 |
r_angle_other_deg | 0.956 |
r_chiral_restr | 0.073 |
r_bond_refined_d | 0.014 |
r_gen_planes_refined | 0.007 |
r_gen_planes_other | 0.004 |
r_bond_other_d | 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 |
---|
Non-Hydrogen Atoms | Number |
---|
Protein Atoms | 9347 |
Nucleic Acid Atoms | |
Solvent Atoms | 146 |
Heterogen Atoms | 909 |
Software
Software |
---|
Software Name | Purpose |
---|
REFMAC | refinement |
CrystFEL | data reduction |
CrystFEL | data scaling |
PHASER | phasing |