5NJ4

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 2I5N 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.8277Macrocrystal 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 = 226.5α = 90
b = 226.5β = 90
c = 113.9γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray298PIXELCS-PAD CXI-12016-06-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1FREE ELECTRON LASERSLAC LCLS BEAMLINE CXI1.307SLAC LCLSCXI

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)CC (Half)R Split (All)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
12.435.71000.9970.048611.21529118454
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)R Split (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.42.461000.4381.06106

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 REPLACEMENTTHROUGHOUT2I5N2.435.7109673571199.950.162140.160860.18632RANDOM81.496
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]
1.211.21-2.42
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.56
r_dihedral_angle_4_deg14.767
r_dihedral_angle_3_deg13.641
r_long_range_B_refined7.989
r_long_range_B_other7.989
r_scangle_other6.065
r_dihedral_angle_1_deg5.749
r_mcangle_other5.29
r_mcangle_it5.289
r_scbond_it3.921
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.56
r_dihedral_angle_4_deg14.767
r_dihedral_angle_3_deg13.641
r_long_range_B_refined7.989
r_long_range_B_other7.989
r_scangle_other6.065
r_dihedral_angle_1_deg5.749
r_mcangle_other5.29
r_mcangle_it5.289
r_scbond_it3.921
r_scbond_other3.921
r_mcbond_it3.547
r_mcbond_other3.543
r_angle_refined_deg1.96
r_angle_other_deg0.956
r_chiral_restr0.073
r_bond_refined_d0.014
r_gen_planes_refined0.007
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 Atoms146
Heterogen Atoms909

Software

Software
Software NamePurpose
REFMACrefinement
CrystFELdata reduction
CrystFELdata scaling
PHASERphasing