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Time-resolved SFX structure of the PR intermediate of cytochrome c oxidase at room temperature
Serial Crystallography (SX)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2DYR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 BATCH MODE 6.8 277 36 hour crystallization in a cold room with stirring
Crystal Properties Matthews coefficient Solvent content 4.4 72.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 178.7 α = 90 b = 189.8 β = 90 c = 211.3 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 293 PIXEL CS-PAD XPP 2016-12-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 FREE ELECTRON LASER SLAC LCLS BEAMLINE MFX 1.306 SLAC LCLS MFX
Serial Crystallography Sample delivery method Diffraction ID Description Sample Delivery Method 1 injection
Measurement Diffraction ID Pulse Duration Pulse Repetition Rate Focal Spot Size Pulse Energy Photons Per Pulse 1 40 (fs) 120 9.5 (KeV)
Data Reduction Diffraction ID Frames Indexed Crystal Hits Frames Indexed Latices Merged 1 98993 108241 98993
Injection Diffraction ID Description Flow Rate Injector Diameter Injection Power Injector Nozzle Filter Size Carrier Solvent 1 GDVN undefined (µl/min) undefined (µm)
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 2.5 10.5 98.54 0.989 5.1 1038 231448
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 2.5 2.561 100 0.168 0.56
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 2dyr 2.5 10.5 231448 12143 98.54 0.17777 0.17565 0.1847 0.21736 0.2206 RANDOM 63.44
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] -2.5 0.95 1.55
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.896 r_dihedral_angle_3_deg 17.771 r_dihedral_angle_4_deg 17.572 r_long_range_B_refined 11.656 r_long_range_B_other 11.656 r_scangle_other 8.667 r_mcangle_it 7.367 r_mcangle_other 7.367 r_dihedral_angle_1_deg 7.099 r_scbond_it 5.517
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.896 r_dihedral_angle_3_deg 17.771 r_dihedral_angle_4_deg 17.572 r_long_range_B_refined 11.656 r_long_range_B_other 11.656 r_scangle_other 8.667 r_mcangle_it 7.367 r_mcangle_other 7.367 r_dihedral_angle_1_deg 7.099 r_scbond_it 5.517 r_scbond_other 5.517 r_mcbond_it 4.834 r_mcbond_other 4.829 r_angle_refined_deg 1.696 r_angle_other_deg 1.388 r_chiral_restr 0.155 r_gen_planes_other 0.017 r_gen_planes_refined 0.01 r_bond_refined_d 0.008 r_bond_other_d 0.005 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 28419 Nucleic Acid Atoms Solvent Atoms 772 Heterogen Atoms 2228
Software Software Software Name Purpose REFMAC refinement CrystFEL data reduction CrystFEL data scaling PHASER phasing