Navigation Tabs 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 5NJ4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.8 277 Crystals grown from one round of seeding.
Macrocrystal growth:
25 ul sitting drop. 10 ul 10 mg/ml protein, 15 ul precipitate solution
Precipitate solution: 3.6 M Ammonium sulphate, 20 mM sodium phosphate buffer pH 6.8. 6 % w:v heptane-1-2-3-triol.
1 ml 2 M Ammonium sulphate reservoir
Growth at 277 K for 4 days.
Macrocrystals crushed into seed stock
Micro-crystals
17.5 ul sitting drop. 10 ul 8.5 mg/ml protein, 7.5 ul precipitate solution
1 ml 2 M Ammonium sulphate solution
Crystal Properties Matthews coefficient Solvent content 5.52 77.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 226.4 α = 90 b = 226.4 β = 90 c = 113.7 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 293 PIXEL CS-PAD CXI-1 2015-04-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 FREE ELECTRON LASER SLAC LCLS BEAMLINE CXI 1.89 SLAC LCLS CXI
Data Collection Overall 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 1 2.8 36.9 100 0.997 10.4 1342 69325 97.4
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.8 2.89 100 0.408 0.88 361
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 5NJ4 2.8 36.9 69325 3626 99.94 0.16665 0.16507 0.19612 RANDOM 96.859
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] 1.6 1.6 -3.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.947 r_dihedral_angle_4_deg 15.906 r_dihedral_angle_3_deg 14.97 r_long_range_B_refined 10.051 r_long_range_B_other 10.051 r_scangle_other 8.063 r_mcangle_other 7.311 r_mcangle_it 7.31 r_dihedral_angle_1_deg 6.101 r_scbond_it 5.488
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.947 r_dihedral_angle_4_deg 15.906 r_dihedral_angle_3_deg 14.97 r_long_range_B_refined 10.051 r_long_range_B_other 10.051 r_scangle_other 8.063 r_mcangle_other 7.311 r_mcangle_it 7.31 r_dihedral_angle_1_deg 6.101 r_scbond_it 5.488 r_scbond_other 5.488 r_mcbond_it 5.24 r_mcbond_other 5.237 r_angle_refined_deg 2.052 r_angle_other_deg 0.987 r_chiral_restr 0.077 r_bond_refined_d 0.015 r_gen_planes_refined 0.008 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 13 Heterogen Atoms 836
Software Software Software Name Purpose REFMAC refinement CrystFEL data reduction CrystFEL data scaling PHASER phasing
