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Membrane Protein Megahertz Crystallography at the European XFEL, Photosystem I at synchrotron to 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 MICRODIALYSIS 6.4 283 MES 5 mM
5- 30 mM MgSO4
0.02 % beta-DDM
Crystal Properties Matthews coefficient Solvent content 79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 278.496 α = 90 b = 165.126 β = 119.42 c = 283.427 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 100 CCD ADSC QUANTUM 315 2005-04-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.2 0.987 ALS 5.0.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) CC (Half) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.9 48.87 99.7 0.136 0.966 7.1 3.6 492002
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) Redundancy Number Unique Reflections (All) 1 2.9 2.95 100 0.481 0.684 2.5 3.5
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 48.87 467047 24873 99.61 0.30537 0.30334 0.3073 0.34306 0.3453 RANDOM 43.362
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] 1.06 1.97 -5.03 1.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.652 r_dihedral_angle_3_deg 17.804 r_dihedral_angle_4_deg 17.795 r_dihedral_angle_1_deg 7.167 r_long_range_B_refined 4.603 r_long_range_B_other 4.603 r_mcangle_it 3.672 r_mcangle_other 3.672 r_scangle_other 2.817 r_angle_refined_deg 2.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.652 r_dihedral_angle_3_deg 17.804 r_dihedral_angle_4_deg 17.795 r_dihedral_angle_1_deg 7.167 r_long_range_B_refined 4.603 r_long_range_B_other 4.603 r_mcangle_it 3.672 r_mcangle_other 3.672 r_scangle_other 2.817 r_angle_refined_deg 2.26 r_mcbond_it 2.251 r_mcbond_other 2.251 r_scbond_it 1.754 r_scbond_other 1.754 r_angle_other_deg 1.519 r_chiral_restr 0.097 r_gen_planes_other 0.012 r_gen_planes_refined 0.01 r_bond_refined_d 0.007 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 276 Heterogen Atoms 19976
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing