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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 (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) 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 0.1679 0.18632 0.1901 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