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Membrane Protein Megahertz Crystallography at the European XFEL, Photosystem I XFEL at 2.9 A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1JB0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 BATCH MODE 6.4 283 0-3 mM MgSO4
5 mM MES
0.02 % beta-DDM
Crystal Properties Matthews coefficient Solvent content 79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 279.1 α = 90 b = 164.6 β = 119.25 c = 284.1 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 298 PIXEL AGIPD 2017-11-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 FREE ELECTRON LASER EUROPEAN XFEL BEAMLINE SPB/SFX 1.399 European XFEL SPB/SFX
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 2.9 39.88 99.4 0.92 3.5 94 493312 61
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 2.9 3 93.9 0.023 0.47 52
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 (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1JB0 2.9 39.88 467105 24635 99.26 0.3 0.29809 0.3005 0.33596 0.3371 RANDOM 55.964
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] 0.78 0.36 -1.37 0.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.143 r_dihedral_angle_3_deg 17.758 r_dihedral_angle_4_deg 17.209 r_dihedral_angle_1_deg 7.131 r_long_range_B_refined 5.374 r_long_range_B_other 5.374 r_mcangle_it 4.453 r_mcangle_other 4.453 r_scangle_other 3.384 r_mcbond_it 2.709
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.143 r_dihedral_angle_3_deg 17.758 r_dihedral_angle_4_deg 17.209 r_dihedral_angle_1_deg 7.131 r_long_range_B_refined 5.374 r_long_range_B_other 5.374 r_mcangle_it 4.453 r_mcangle_other 4.453 r_scangle_other 3.384 r_mcbond_it 2.709 r_mcbond_other 2.709 r_angle_refined_deg 2.21 r_scbond_it 2.07 r_scbond_other 2.07 r_angle_other_deg 1.535 r_chiral_restr 0.095 r_gen_planes_other 0.012 r_gen_planes_refined 0.01 r_bond_refined_d 0.006 r_bond_other_d 0.003 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 Atoms Number Protein Atoms 52485 Nucleic Acid Atoms Solvent Atoms 71 Heterogen Atoms 19976
Software Software Software Name Purpose REFMAC refinement CrystFEL data reduction CrystFEL data scaling PHASER phasing