5O4C

From macrocrystals to microcrystals: a strategy for membrane protein serial crystallography


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5NJ4 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.8277Crystals 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 coefficientSolvent content
5.5277.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 226.4α = 90
b = 226.4β = 90
c = 113.7γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray293PIXELCS-PAD CXI-12015-04-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1FREE ELECTRON LASERSLAC LCLS BEAMLINE CXI1.89SLAC LCLSCXI

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)CC (Half)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.836.91000.99710.413426932597.4
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.82.891000.4080.88361

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT5NJ42.836.969325362699.940.166650.165070.19612RANDOM96.859
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]
1.61.6-3.21
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.947
r_dihedral_angle_4_deg15.906
r_dihedral_angle_3_deg14.97
r_long_range_B_refined10.051
r_long_range_B_other10.051
r_scangle_other8.063
r_mcangle_other7.311
r_mcangle_it7.31
r_dihedral_angle_1_deg6.101
r_scbond_it5.488
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.947
r_dihedral_angle_4_deg15.906
r_dihedral_angle_3_deg14.97
r_long_range_B_refined10.051
r_long_range_B_other10.051
r_scangle_other8.063
r_mcangle_other7.311
r_mcangle_it7.31
r_dihedral_angle_1_deg6.101
r_scbond_it5.488
r_scbond_other5.488
r_mcbond_it5.24
r_mcbond_other5.237
r_angle_refined_deg2.052
r_angle_other_deg0.987
r_chiral_restr0.077
r_bond_refined_d0.015
r_gen_planes_refined0.008
r_gen_planes_other0.004
r_bond_other_d0.002
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 AtomsNumber
Protein Atoms9347
Nucleic Acid Atoms
Solvent Atoms13
Heterogen Atoms836

Software

Software
Software NamePurpose
REFMACrefinement
CrystFELdata reduction
CrystFELdata scaling
PHASERphasing