6PGK

Membrane Protein Megahertz Crystallography at the European XFEL, Photosystem I XFEL at 2.9 A


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1JB0 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1BATCH MODE6.42830-3 mM MgSO4 5 mM MES 0.02 % beta-DDM
Crystal Properties
Matthews coefficientSolvent content
79

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 279.1α = 90
b = 164.6β = 119.25
c = 284.1γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray298PIXELAGIPD2017-11-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1FREE ELECTRON LASEREUROPEAN XFEL BEAMLINE SPB/SFX1.399European XFELSPB/SFX

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
12.939.8899.40.923.59449331261
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)
12.9393.90.0230.4752

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 REPLACEMENTTHROUGHOUT1JB02.939.884671052463599.260.30.298090.33596RANDOM55.964
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]
0.780.36-1.370.11
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.143
r_dihedral_angle_3_deg17.758
r_dihedral_angle_4_deg17.209
r_dihedral_angle_1_deg7.131
r_long_range_B_refined5.374
r_long_range_B_other5.374
r_mcangle_it4.453
r_mcangle_other4.453
r_scangle_other3.384
r_mcbond_it2.709
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.143
r_dihedral_angle_3_deg17.758
r_dihedral_angle_4_deg17.209
r_dihedral_angle_1_deg7.131
r_long_range_B_refined5.374
r_long_range_B_other5.374
r_mcangle_it4.453
r_mcangle_other4.453
r_scangle_other3.384
r_mcbond_it2.709
r_mcbond_other2.709
r_angle_refined_deg2.21
r_scbond_it2.07
r_scbond_other2.07
r_angle_other_deg1.535
r_chiral_restr0.095
r_gen_planes_other0.012
r_gen_planes_refined0.01
r_bond_refined_d0.006
r_bond_other_d0.003
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 Atoms52485
Nucleic Acid Atoms
Solvent Atoms71
Heterogen Atoms19976

Software

Software
Software NamePurpose
REFMACrefinement
CrystFELdata reduction
CrystFELdata scaling
PHASERphasing