6PFY

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


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1MICRODIALYSIS6.4283MES 5 mM 5- 30 mM MgSO4 0.02 % beta-DDM
Crystal Properties
Matthews coefficientSolvent content
79

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 278.496α = 90
b = 165.126β = 119.42
c = 283.427γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152005-04-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 5.0.20.987ALS5.0.2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
12.948.8799.70.1360.9667.13.6492002
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.92.951000.4810.6842.53.5

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 REPLACEMENTTHROUGHOUT1jb02.948.874670472487399.610.305370.303340.34306RANDOM43.362
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]
1.061.97-5.031.07
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.652
r_dihedral_angle_3_deg17.804
r_dihedral_angle_4_deg17.795
r_dihedral_angle_1_deg7.167
r_long_range_B_refined4.603
r_long_range_B_other4.603
r_mcangle_it3.672
r_mcangle_other3.672
r_scangle_other2.817
r_angle_refined_deg2.26
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.652
r_dihedral_angle_3_deg17.804
r_dihedral_angle_4_deg17.795
r_dihedral_angle_1_deg7.167
r_long_range_B_refined4.603
r_long_range_B_other4.603
r_mcangle_it3.672
r_mcangle_other3.672
r_scangle_other2.817
r_angle_refined_deg2.26
r_mcbond_it2.251
r_mcbond_other2.251
r_scbond_it1.754
r_scbond_other1.754
r_angle_other_deg1.519
r_chiral_restr0.097
r_gen_planes_other0.012
r_gen_planes_refined0.01
r_bond_refined_d0.007
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 Atoms276
Heterogen Atoms19976

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing